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/7786230/working' mkdir: created directory `/scratch/stefan/7786230/working/protonate' Storing results in /scratch/stefan/7786230/finished Working in /scratch/stefan/7786230/working /scratch/stefan/7786230/working /scratch/stefan/7786230 /scratch/stefan/7786230/working/protonate /scratch/stefan/7786230/working /scratch/stefan/7786230 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory Dec 03, 2019 1:11:52 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1084 protomers created Coalesing and merging protomers 1041 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1064 protomers after new stereo-center expansion /scratch/stefan/7786230/working /scratch/stefan/7786230 Bulk generating 3D conformations all protomers in /scratch/stefan/7786230/working/3D mkdir: created directory `/scratch/stefan/7786230/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7786230/working/protonate/xaaaaef-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' 1065 3D conformations generated for 1000 compounds Building REAL300024450150 mkdir: created directory `/scratch/stefan/7786230/working/building' mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450150' /scratch/stefan/7786230/working/building/REAL300024450150 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450150 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450150/0 /scratch/stefan/7786230/working/building/REAL300024450150 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1 `/scratch/stefan/7786230/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1) `REAL300024450150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450150/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450150 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 41, 123, 123, 123, 123, 123, 1, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 123, 1, 2, 2, 2, 10] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 22 ./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: REAL300024450150 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 192, 192, 192, 123, 123, 123, 123, 123, 118, 50, 118, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 201, 192, 123, 123, 123, 123, 123, 123, 123, 50, 50, 1, 123, 123, 123, 123, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 624 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450150 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 10, 10, 10, 10, 10, 18, 18, 57, 118, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 57, 57, 201, 10, 10, 10, 10, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 463 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450150 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450150 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `/scratch/stefan/7786230/finished' Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450150/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450150 Building REAL300024450151 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450151' /scratch/stefan/7786230/working/building/REAL300024450151 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450151 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450151/0 /scratch/stefan/7786230/working/building/REAL300024450151 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/2 `/scratch/stefan/7786230/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450151/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450151 none CCOC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 117, 200, 187, 117, 117, 99, 99, 99, 99, 99, 90, 30, 90, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 200, 201, 201, 201, 201, 201, 117, 99, 99, 99, 99, 99, 99, 99, 30, 30, 1, 99, 99, 99, 99] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 826 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450151 none CCOC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 13, 3, 13, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 99, 99, 99, 99, 99, 1, 1, 18, 18, 18, 18, 18, 13, 22, 22, 22, 22, 22, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 99, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450151 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450151 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450151/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450151 Building REAL300024450152 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450152' /scratch/stefan/7786230/working/building/REAL300024450152 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450152 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450152/0 /scratch/stefan/7786230/working/building/REAL300024450152 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/3 `/scratch/stefan/7786230/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450152/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450152 none CC1C(NC(=O)CC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 82, 82, 82, 201, 201, 201, 201, 67, 67, 67, 67, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 82, 201, 201, 67, 67, 67, 67, 67, 67, 39, 39, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 776 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450152 none CC1C(NC(=O)CC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 10, 22, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 3, 17, 17, 1, 1, 1, 1, 1, 1, 10, 10, 67] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450152 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450152 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450152/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450152 Building REAL300024450153 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450153' /scratch/stefan/7786230/working/building/REAL300024450153 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450153 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450153/0 /scratch/stefan/7786230/working/building/REAL300024450153 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/4 `/scratch/stefan/7786230/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450153/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450153 none COC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 5 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 9 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450153 none COC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 5 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450153 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450153 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450153/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450153 Building REAL300024450154 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450154' /scratch/stefan/7786230/working/building/REAL300024450154 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450154 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450154/0 /scratch/stefan/7786230/working/building/REAL300024450154 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/5 `/scratch/stefan/7786230/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450154/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450154 none CC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 157, 81, 81, 81, 69, 69, 69, 69, 69, 67, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 157, 157, 81, 69, 69, 69, 69, 69, 69, 69, 27, 27, 1, 69, 69, 69, 69] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 722 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450154 none CC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 39, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 69, 69, 69, 69, 69, 1, 1, 39, 39, 39, 39, 39, 39, 39, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450154 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450154 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450154/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450154 Building REAL300024450155 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450155' /scratch/stefan/7786230/working/building/REAL300024450155 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450155 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450155/0 /scratch/stefan/7786230/working/building/REAL300024450155 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/6 `/scratch/stefan/7786230/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450155/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450155 none CC(OCC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 10, 22, 45, 45, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 72, 72, 72, 72, 72, 1, 1, 6, 6, 6, 6, 22, 22, 45, 45, 45, 45, 45, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 72, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 281 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: REAL300024450155 none CC(OCC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 87, 139, 158, 176, 201, 201, 87, 87, 72, 72, 72, 72, 72, 71, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 139, 139, 139, 139, 176, 176, 201, 201, 201, 201, 201, 87, 72, 72, 72, 72, 72, 72, 72, 28, 28, 1, 72, 72, 72, 72] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 792 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450155 none CC(OCC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 7, 1, 1, 1, 1, 30, 39, 39, 39, 45, 45, 45, 45, 45, 65, 65, 97, 140, 201, 201, 201, 201, 201, 45, 45, 30, 30, 30, 30, 7, 7, 1, 1, 1, 1, 1, 39, 45, 45, 45, 45, 45, 45, 45, 97, 97, 201, 45, 45, 45, 45] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 35, 36, 37] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 592 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450155 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450155 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450155/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450155 Building REAL300024450156 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450156' /scratch/stefan/7786230/working/building/REAL300024450156 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450156 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450156/0 /scratch/stefan/7786230/working/building/REAL300024450156 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/7 `/scratch/stefan/7786230/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450156/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450156 none CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 199, 178, 74, 74, 74, 64, 64, 64, 64, 64, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 178, 178, 74, 64, 64, 64, 64, 64, 64, 64, 30, 30, 1, 64, 64, 64, 64] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 777 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450156 none CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 16, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 64, 64, 64, 64, 64, 1, 1, 39, 39, 39, 39, 39, 25, 25, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 272 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450156 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450156 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450156/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450156 Building REAL300024450157 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450157' /scratch/stefan/7786230/working/building/REAL300024450157 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450157 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450157/0 /scratch/stefan/7786230/working/building/REAL300024450157 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/8 `/scratch/stefan/7786230/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450157/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450157 none CCCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 148, 135, 124, 74, 124, 74, 74, 64, 64, 64, 64, 64, 63, 29, 63, 12, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 148, 148, 124, 124, 124, 124, 74, 64, 64, 64, 64, 64, 64, 64, 29, 29, 1, 64, 64, 64, 64] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 898 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450157 none CCCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 23, 12, 7, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 64, 64, 64, 64, 64, 1, 1, 43, 43, 43, 43, 43, 43, 43, 23, 23, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450157 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450157 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450157/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450157 Building REAL300024450158 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450158' /scratch/stefan/7786230/working/building/REAL300024450158 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450158 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450158/0 /scratch/stefan/7786230/working/building/REAL300024450158 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/9 `/scratch/stefan/7786230/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450158/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450158 none C=CCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 149, 121, 114, 67, 114, 67, 67, 61, 61, 61, 61, 61, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 149, 149, 114, 114, 114, 114, 67, 61, 61, 61, 61, 61, 61, 61, 28, 28, 1, 61, 61, 61, 61] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 924 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450158 none C=CCCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 15, 9, 7, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 61, 61, 61, 61, 61, 1, 1, 42, 42, 42, 29, 29, 15, 15, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450158 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450158 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450158/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450158 Building REAL300024450159 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450159' /scratch/stefan/7786230/working/building/REAL300024450159 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450159 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450159/0 /scratch/stefan/7786230/working/building/REAL300024450159 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/10 `/scratch/stefan/7786230/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450159/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450159 none CC1C(NC(=O)C2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 53, 103, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 53, 53, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 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: REAL300024450159 none CC1C(NC(=O)C2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 90, 90, 90, 201, 201, 201, 201, 75, 75, 75, 73, 43, 73, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 90, 201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75, 75, 75, 43, 43, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 626 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450159 none CC1C(NC(=O)C2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 25, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 75] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450159 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450159 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450159/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450159 Building REAL300024450160 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450160' /scratch/stefan/7786230/working/building/REAL300024450160 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450160 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450160/0 /scratch/stefan/7786230/working/building/REAL300024450160 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/11 `/scratch/stefan/7786230/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=NC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450160/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450160 none CC1C(NC(=O)C2=CC=NC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 44, 100, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 44, 44, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 410 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: REAL300024450160 none CC1C(NC(=O)C2=CC=NC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 96, 96, 103, 103, 103, 201, 201, 201, 201, 201, 201, 96, 96, 96, 95, 48, 95, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 103, 201, 201, 201, 96, 96, 96, 96, 96, 96, 48, 48, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 472 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450160 none CC1C(NC(=O)C2=CC=NC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 35, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 3, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 96] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450160 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450160 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450160/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450160 Building REAL300024450161 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450161' /scratch/stefan/7786230/working/building/REAL300024450161 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450161 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450161/0 /scratch/stefan/7786230/working/building/REAL300024450161 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/12 `/scratch/stefan/7786230/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1) `REAL300024450161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450161/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450161 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 23, 70, 70, 70, 70, 70, 1, 1, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 70, 1, 2, 2, 2] 93 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 153 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: REAL300024450161 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 85, 85, 85, 70, 70, 70, 70, 70, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 93, 93, 93, 93, 93, 85, 70, 70, 70, 70, 70, 70, 70, 37, 37, 1, 70, 70, 70, 70] 93 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 300 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450161 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 14, 14, 36, 49, 93, 93, 93, 93, 93, 10, 10, 1, 2, 2, 2, 1, 6, 10, 10, 10, 10, 10, 10, 10, 36, 36, 93, 10, 10, 10, 10] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 240 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450161 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450161 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450161/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450161 Building REAL300024450162 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450162' /scratch/stefan/7786230/working/building/REAL300024450162 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450162 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450162/0 /scratch/stefan/7786230/working/building/REAL300024450162 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/13 `/scratch/stefan/7786230/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450162/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450162 none CC1C(NC(=O)C2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 50, 104, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 4, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 50, 50, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 440 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: REAL300024450162 none CC1C(NC(=O)C2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [123, 123, 123, 123, 199, 199, 199, 201, 201, 201, 201, 201, 123, 123, 123, 119, 59, 119, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 199, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 59, 59, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 634 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450162 none CC1C(NC(=O)C2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 42, 123, 123, 123, 123, 123, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 123] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450162 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450162 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450162/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450162 Building REAL300024450163 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450163' /scratch/stefan/7786230/working/building/REAL300024450163 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450163 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450163/0 /scratch/stefan/7786230/working/building/REAL300024450163 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/14 `/scratch/stefan/7786230/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450163/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450163 none CCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 6 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 15 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450163 none CCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 6 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 33 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450163 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450163 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450163/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450163 Building REAL300024450164 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450164' /scratch/stefan/7786230/working/building/REAL300024450164 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450164 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450164/0 /scratch/stefan/7786230/working/building/REAL300024450164 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/15 `/scratch/stefan/7786230/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450164/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450164 none COCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 181, 170, 155, 51, 51, 51, 43, 43, 43, 43, 43, 42, 25, 42, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 201, 201, 181, 181, 181, 181, 155, 155, 51, 43, 43, 43, 43, 43, 43, 43, 25, 25, 1, 43, 43, 43, 43] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 917 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450164 none COCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 19, 17, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 43, 43, 43, 43, 43, 1, 1, 34, 34, 34, 34, 34, 19, 19, 19, 19, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 43, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450164 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450164 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450164/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450164 Building REAL300024450165 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450165' /scratch/stefan/7786230/working/building/REAL300024450165 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450165 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450165/0 /scratch/stefan/7786230/working/building/REAL300024450165 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/16 `/scratch/stefan/7786230/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450165/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450165 none CCCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 63, 63, 63, 50, 50, 50, 50, 50, 49, 25, 49, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 63, 50, 50, 50, 50, 50, 50, 50, 25, 25, 1, 50, 50, 50, 50] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 811 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450165 none CCCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 29, 15, 28, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 50, 50, 50, 50, 50, 1, 1, 37, 37, 37, 37, 37, 37, 37, 29, 29, 29, 29, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450165 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450165 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450165/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450165 Building REAL300024450166 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450166' /scratch/stefan/7786230/working/building/REAL300024450166 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450166 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450166/0 /scratch/stefan/7786230/working/building/REAL300024450166 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/17 `/scratch/stefan/7786230/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450166/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450166 none COC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 198, 201, 82, 82, 82, 70, 70, 70, 70, 70, 66, 29, 66, 12, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 198, 198, 82, 70, 70, 70, 70, 70, 70, 70, 29, 29, 1, 70, 70, 70, 70] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 738 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450166 none COC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 25, 17, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 70, 70, 70, 70, 70, 1, 1, 28, 28, 28, 25, 25, 25, 25, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 70, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 236 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450166 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450166 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450166/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450166 Building REAL300024450167 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450167' /scratch/stefan/7786230/working/building/REAL300024450167 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450167 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450167/0 /scratch/stefan/7786230/working/building/REAL300024450167 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/18 `/scratch/stefan/7786230/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450167/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450167 none CC1C(NC(=O)CC2=CN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 38, 38, 86, 131, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 19, 7, 7, 1, 2, 2, 2, 1, 36, 36, 36, 36, 36, 36, 86, 86, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 576 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: REAL300024450167 none CC1C(NC(=O)CC2=CN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 35, 55, 55, 55, 130, 201, 201, 201, 201, 201, 35, 35, 35, 34, 25, 34, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 55, 130, 130, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 35, 25, 25, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 654 number of broken/clashed sets: 49 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450167 none CC1C(NC(=O)CC2=CN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 6, 10, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 4, 12, 12, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 6, 6, 35] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450167 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450167 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450167/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450167 Building REAL300024450168 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450168' /scratch/stefan/7786230/working/building/REAL300024450168 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450168 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450168/0 /scratch/stefan/7786230/working/building/REAL300024450168 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/19 `/scratch/stefan/7786230/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450168/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450168 none CC1C(NC(=O)C2CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 28, 28, 77, 108, 178, 178, 178, 178, 178, 19, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 77, 77, 178] 178 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 45, 44, 11, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 487 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: REAL300024450168 none CC1C(NC(=O)C2CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 87, 87, 87, 178, 178, 178, 178, 178, 178, 61, 61, 61, 58, 38, 58, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 87, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 61, 61, 61, 61, 61, 61, 38, 38, 1] 178 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 591 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450168 none CC1C(NC(=O)C2CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 13, 21, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 13, 13, 61] 178 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 167 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450168 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450168 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450168/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450168 Building REAL300024450169 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450169' /scratch/stefan/7786230/working/building/REAL300024450169 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450169 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450169/0 /scratch/stefan/7786230/working/building/REAL300024450169 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/20 `/scratch/stefan/7786230/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450169/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450169 none C=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 77, 77, 77, 75, 75, 75, 75, 75, 66, 25, 66, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 196, 196, 77, 75, 75, 75, 75, 75, 75, 75, 25, 25, 1, 75, 75, 75, 75] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 761 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450169 none C=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 16, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 75, 75, 75, 75, 75, 1, 1, 31, 31, 31, 16, 16, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 75, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 242 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450169 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450169 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450169/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450169 Building REAL300024450170 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450170' /scratch/stefan/7786230/working/building/REAL300024450170 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450170 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450170/0 /scratch/stefan/7786230/working/building/REAL300024450170 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/21 `/scratch/stefan/7786230/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450170/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450170 none CC1C(NC(=O)C2=COCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 41, 41, 100, 131, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 12, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 100, 100, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 562 number of broken/clashed sets: 33 ./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: REAL300024450170 none CC1C(NC(=O)C2=COCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 127, 127, 127, 201, 201, 201, 201, 201, 89, 89, 89, 84, 40, 84, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 127, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 40, 40, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 544 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450170 none CC1C(NC(=O)C2=COCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 15, 26, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 15, 15, 89] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450170 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450170 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450170/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450170 Building REAL300024450171 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450171' /scratch/stefan/7786230/working/building/REAL300024450171 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450171 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450171/0 /scratch/stefan/7786230/working/building/REAL300024450171 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/22 `/scratch/stefan/7786230/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450171/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450171 none COC(=O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 16, 36, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 41, 41, 41, 41, 41, 1, 1, 36, 36, 36, 16, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 43 ./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: REAL300024450171 none COC(=O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 112, 201, 112, 112, 44, 44, 44, 41, 41, 41, 41, 41, 38, 25, 38, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 112, 112, 112, 112, 44, 41, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 41, 41] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 627 number of broken/clashed sets: 43 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450171 none COC(=O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 4, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 16, 16, 19, 19, 46, 67, 112, 112, 112, 112, 112, 16, 16, 4, 4, 4, 1, 1, 1, 1, 11, 16, 16, 16, 16, 16, 16, 16, 46, 46, 112, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 30, 31] set([0, 1, 3, 8, 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, 48]) total number of confs: 302 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450171 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450171 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450171/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450171 Building REAL300024450172 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450172' /scratch/stefan/7786230/working/building/REAL300024450172 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450172 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450172/0 /scratch/stefan/7786230/working/building/REAL300024450172 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/23 `/scratch/stefan/7786230/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450172/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450172 none CC1C(NC(=O)C2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 33, 33, 72, 98, 153, 153, 153, 153, 153, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 72, 72, 153] 153 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 426 number of broken/clashed sets: 28 ./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: REAL300024450172 none CC1C(NC(=O)C2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 84, 84, 84, 153, 153, 153, 153, 153, 65, 65, 65, 61, 39, 61, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 84, 153, 153, 153, 153, 153, 153, 153, 153, 153, 65, 65, 65, 65, 65, 65, 39, 39, 1] 153 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 492 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450172 none CC1C(NC(=O)C2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 13, 21, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 13, 13, 65] 153 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450172 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450172 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450172/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450172 Building REAL300024450173 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450173' /scratch/stefan/7786230/working/building/REAL300024450173 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450173 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450173/0 /scratch/stefan/7786230/working/building/REAL300024450173 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/24 `/scratch/stefan/7786230/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450173/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450173 none CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 191, 86, 86, 86, 63, 63, 63, 63, 63, 61, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 191, 191, 86, 63, 63, 63, 63, 63, 63, 63, 27, 27, 1, 63, 63, 63, 63] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 785 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450173 none CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 21, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 63, 63, 63, 63, 63, 1, 1, 29, 29, 29, 29, 29, 21, 21, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450173 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450173 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450173/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450173 Building REAL300024450174 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450174' /scratch/stefan/7786230/working/building/REAL300024450174 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450174 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450174/0 /scratch/stefan/7786230/working/building/REAL300024450174 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/25 `/scratch/stefan/7786230/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450174/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450174 none CCNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 185, 185, 179, 185, 179, 83, 83, 83, 63, 63, 63, 63, 63, 62, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 185, 179, 179, 179, 179, 83, 63, 63, 63, 63, 63, 63, 63, 28, 28, 1, 63, 63, 63, 63] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 796 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450174 none CCNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 19, 19, 11, 19, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 63, 63, 63, 63, 63, 1, 1, 32, 32, 32, 32, 32, 19, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450174 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450174 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450174/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450174 Building REAL300024450175 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450175' /scratch/stefan/7786230/working/building/REAL300024450175 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450175 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450175/0 /scratch/stefan/7786230/working/building/REAL300024450175 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/26 `/scratch/stefan/7786230/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450175/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450175 none CC1C(NC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 50, 108, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 50, 50, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 22 ./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: REAL300024450175 none CC1C(NC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 165, 165, 165, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 156, 66, 156, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 201, 201, 201, 165, 165, 165, 165, 165, 165, 66, 66, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 615 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450175 none CC1C(NC(=O)C2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 16, 51, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 6, 8, 8, 1, 1, 1, 1, 1, 1, 16, 16, 165] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 275 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450175 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450175 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450175/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450175 Building REAL300024450176 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450176' /scratch/stefan/7786230/working/building/REAL300024450176 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450176 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450176/0 /scratch/stefan/7786230/working/building/REAL300024450176 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/27 `/scratch/stefan/7786230/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450176/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450176 none COCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 194, 100, 194, 100, 100, 73, 73, 73, 73, 73, 69, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 194, 194, 194, 194, 100, 73, 73, 73, 73, 73, 73, 73, 28, 28, 1, 73, 73, 73, 73] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 795 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450176 none COCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 24, 15, 4, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 73, 73, 73, 73, 73, 1, 1, 33, 33, 33, 24, 24, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 73, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450176 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450176 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450176/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450176 Building REAL300024450177 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450177' /scratch/stefan/7786230/working/building/REAL300024450177 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450177 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450177/0 /scratch/stefan/7786230/working/building/REAL300024450177 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/28 `/scratch/stefan/7786230/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450177/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450177 none CC1C(NC(=O)CCCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 59, 59, 59, 171, 176, 201, 201, 176, 201, 43, 43, 43, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 59, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 43, 28, 28, 1] 201 rigid atoms, others: [56, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1155 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450177 none CC1C(NC(=O)CCCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 18, 26, 30, 31, 27, 31, 1, 1, 1, 1, 1, 3, 3, 6, 10, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 4, 18, 18, 30, 30, 30, 30, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 6, 43] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 15, 16, 49, 50, 51, 52, 53, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450177 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450177 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450177/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450177 Building REAL300024450178 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450178' /scratch/stefan/7786230/working/building/REAL300024450178 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450178 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450178/0 /scratch/stefan/7786230/working/building/REAL300024450178 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/29 `/scratch/stefan/7786230/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450178/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450178 none C=CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 158, 78, 78, 78, 65, 65, 65, 65, 65, 62, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 158, 158, 78, 65, 65, 65, 65, 65, 65, 65, 27, 27, 1, 65, 65, 65, 65] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 847 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450178 none C=CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 25, 12, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 65, 65, 65, 65, 65, 1, 1, 32, 32, 32, 25, 25, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450178 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450178 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450178/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450178 Building REAL300024450179 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450179' /scratch/stefan/7786230/working/building/REAL300024450179 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450179 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450179/0 /scratch/stefan/7786230/working/building/REAL300024450179 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/30 `/scratch/stefan/7786230/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450179/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450179 none CC1C(NC(=O)C2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 4, 1, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 44, 99, 184, 184, 184, 184, 184, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 8, 8, 44, 44, 184] 184 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 383 number of broken/clashed sets: 35 ./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: REAL300024450179 none CC1C(NC(=O)C2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 183, 183, 183, 184, 184, 184, 184, 178, 178, 178, 167, 66, 167, 13, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 183, 184, 184, 178, 178, 178, 178, 178, 178, 66, 66, 1] 184 rigid atoms, others: [41, 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]) total number of confs: 541 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450179 none CC1C(NC(=O)C2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 17, 66, 178, 178, 178, 178, 178, 2, 2, 2, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 17, 17, 178] 184 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 305 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450179 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450179 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450179/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450179 Building REAL300024450180 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450180' /scratch/stefan/7786230/working/building/REAL300024450180 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450180 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450180/0 /scratch/stefan/7786230/working/building/REAL300024450180 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/31 `/scratch/stefan/7786230/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450180/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450180 none CC1C(NC(=O)[C@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 59, 112, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 59, 59, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 454 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: REAL300024450180 none CC1C(NC(=O)[C@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 121, 121, 121, 185, 185, 185, 201, 201, 201, 201, 201, 201, 121, 121, 121, 120, 53, 120, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 185, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 53, 53, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 650 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450180 none CC1C(NC(=O)[C@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 41, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 121] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 232 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450180 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450180 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450180/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450180 Building REAL300024450181 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450181' /scratch/stefan/7786230/working/building/REAL300024450181 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450181 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450181/0 /scratch/stefan/7786230/working/building/REAL300024450181 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/32 `/scratch/stefan/7786230/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450181/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450181 none CC1C(NC(=O)CC2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 27, 27, 7, 27, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 49, 49, 95, 130, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 95, 95, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 553 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: REAL300024450181 none CC1C(NC(=O)CC2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 61, 61, 61, 69, 69, 69, 198, 201, 201, 201, 201, 201, 61, 61, 61, 56, 24, 56, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 69, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 61, 61, 61, 61, 61, 61, 24, 24, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 722 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450181 none CC1C(NC(=O)CC2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 11, 19, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 3, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 11, 11, 61] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450181 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450181 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450181/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450181 Building REAL300024450182 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450182' /scratch/stefan/7786230/working/building/REAL300024450182 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450182 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450182/0 /scratch/stefan/7786230/working/building/REAL300024450182 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/33 `/scratch/stefan/7786230/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450182/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450182 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 29, 83, 83, 83, 83, 83, 1, 1, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 83, 1, 2, 2, 2, 14] 114 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 181 number of broken/clashed sets: 23 ./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: REAL300024450182 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 114, 114, 103, 103, 103, 83, 83, 83, 83, 83, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 114, 114, 114, 114, 114, 103, 83, 83, 83, 83, 83, 83, 83, 39, 39, 1, 83, 83, 83, 83, 114] 114 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 366 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450182 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 18, 18, 48, 67, 114, 114, 114, 114, 114, 14, 14, 1, 2, 2, 2, 1, 6, 14, 14, 14, 14, 14, 14, 14, 48, 48, 114, 14, 14, 14, 14, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 299 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450182 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450182 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450182/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450182 Building REAL300024450183 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450183' /scratch/stefan/7786230/working/building/REAL300024450183 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450183 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450183/0 /scratch/stefan/7786230/working/building/REAL300024450183 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/34 `/scratch/stefan/7786230/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450183/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450183 none CSCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 178, 85, 178, 85, 85, 65, 65, 65, 65, 65, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 197, 197, 178, 178, 178, 178, 85, 65, 65, 65, 65, 65, 65, 65, 29, 29, 1, 65, 65, 65, 65] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 813 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450183 none CSCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 16, 11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 65, 65, 65, 65, 65, 1, 1, 34, 34, 34, 16, 16, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450183 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450183 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450183/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450183 Building REAL300024450184 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450184' /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450184 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450184/0 /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/35 `/scratch/stefan/7786230/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450184/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 6, 6, 7] 7 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 29 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: REAL300024450184 none CC1C(NC(=O)C2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 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, 7, 1] 7 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 13 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 7] 7 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450184/1 /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/36 `/scratch/stefan/7786230/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450184.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450184/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 40, 66, 101, 101, 101, 101, 101, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 40, 40, 101] 101 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 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: REAL300024450184 none CC1C(NC(=O)C2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 98, 98, 98, 101, 101, 101, 101, 101, 101, 72, 72, 72, 71, 49, 71, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 98, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 72, 72, 72, 72, 72, 72, 49, 49, 1] 101 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 344 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 11, 23, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 72] 101 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450184/2 /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/37 `/scratch/stefan/7786230/working/3D/37' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450184.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450184/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 39, 111, 201, 201, 201, 201, 201, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 39, 39, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 405 number of broken/clashed sets: 56 ./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: REAL300024450184 none CC1C(NC(=O)C2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [180, 180, 180, 180, 186, 186, 186, 201, 201, 201, 201, 201, 180, 180, 180, 170, 69, 170, 13, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 180, 69, 69, 1] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 612 number of broken/clashed sets: 56 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450184 none CC1C(NC(=O)C2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 17, 63, 180, 180, 180, 180, 180, 2, 2, 2, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 17, 180] 201 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450184 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450184 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450184/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450184/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450184/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450184 Building REAL300024450185 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450185' /scratch/stefan/7786230/working/building/REAL300024450185 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450185 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450185/0 /scratch/stefan/7786230/working/building/REAL300024450185 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/38 `/scratch/stefan/7786230/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450185/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450185 none CCC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 157, 157, 157, 156, 78, 78, 78, 58, 58, 58, 58, 58, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 157, 156, 156, 78, 58, 58, 58, 58, 58, 58, 58, 27, 27, 1, 58, 58, 58, 58] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 855 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450185 none CCC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 1, 1, 46, 46, 46, 46, 46, 13, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 58, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450185 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450185 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450185/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450185 Building REAL300024450186 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450186' /scratch/stefan/7786230/working/building/REAL300024450186 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450186 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450186/0 /scratch/stefan/7786230/working/building/REAL300024450186 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/39 `/scratch/stefan/7786230/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450186/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450186 none CC1C(NC(=O)C=CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 81, 81, 81, 201, 201, 201, 201, 201, 79, 79, 79, 75, 41, 75, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 79, 79, 79, 41, 41, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 608 number of broken/clashed sets: 47 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450186 none CC1C(NC(=O)C=CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 12, 26, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 3, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 12, 12, 79] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450186 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450186 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450186/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450186 Building REAL300024450187 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450187' /scratch/stefan/7786230/working/building/REAL300024450187 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450187 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450187/0 /scratch/stefan/7786230/working/building/REAL300024450187 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/40 `/scratch/stefan/7786230/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(F)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450187/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450187 none CC1C(NC(=O)C2=CC=C(F)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 50, 102, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 50, 50, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 428 number of broken/clashed sets: 27 ./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: REAL300024450187 none CC1C(NC(=O)C2=CC=C(F)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [140, 140, 140, 140, 159, 159, 159, 201, 201, 201, 201, 201, 201, 140, 140, 140, 137, 64, 137, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 159, 201, 201, 201, 140, 140, 140, 140, 140, 140, 64, 64, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 593 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450187 none CC1C(NC(=O)C2=CC=C(F)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 15, 47, 140, 140, 140, 140, 140, 2, 2, 2, 1, 1, 4, 9, 9, 9, 1, 1, 1, 1, 1, 1, 15, 15, 140] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450187 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450187 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450187/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450187 Building REAL300024450188 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450188' /scratch/stefan/7786230/working/building/REAL300024450188 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450188 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450188/0 /scratch/stefan/7786230/working/building/REAL300024450188 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/41 `/scratch/stefan/7786230/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450188/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450188 none COCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 178, 164, 114, 53, 53, 53, 49, 49, 49, 49, 49, 49, 26, 49, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 178, 178, 114, 114, 53, 49, 49, 49, 49, 49, 49, 49, 26, 26, 1, 49, 49, 49, 49] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 742 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450188 none COCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 22, 17, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 49, 49, 49, 49, 49, 1, 1, 27, 27, 27, 27, 27, 22, 22, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 49, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450188 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450188 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450188/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450188 Building REAL300024450189 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450189' /scratch/stefan/7786230/working/building/REAL300024450189 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450189 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450189/0 /scratch/stefan/7786230/working/building/REAL300024450189 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/42 `/scratch/stefan/7786230/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450189/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450189 none CCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 93, 178, 93, 93, 71, 71, 71, 71, 71, 67, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 178, 93, 71, 71, 71, 71, 71, 71, 71, 29, 29, 1, 71, 71, 71, 71] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 821 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450189 none CCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 18, 5, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 71, 71, 71, 71, 71, 1, 1, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 1, 2, 2, 2] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450189 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450189 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450189/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450189 Building REAL300024450190 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450190' /scratch/stefan/7786230/working/building/REAL300024450190 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450190 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450190/0 /scratch/stefan/7786230/working/building/REAL300024450190 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/43 `/scratch/stefan/7786230/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450190/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450190 none CC1=NN(C)C=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 10, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 28, 71, 71, 71, 71, 71, 1, 1, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 71, 1, 2, 2, 2] 95 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 22 ./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: REAL300024450190 none CC1=NN(C)C=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 95, 95, 95, 95, 95, 76, 76, 76, 71, 71, 71, 71, 71, 64, 35, 64, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 95, 95, 95, 95, 95, 95, 95, 76, 71, 71, 71, 71, 71, 71, 71, 35, 35, 1, 71, 71, 71, 71] 95 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450190 none CC1=NN(C)C=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 11, 11, 11, 11, 11, 15, 15, 40, 57, 95, 95, 95, 95, 95, 11, 11, 2, 2, 2, 2, 2, 2, 1, 8, 11, 11, 11, 11, 11, 11, 11, 40, 40, 95, 11, 11, 11, 11] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 254 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450190 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450190 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450190/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450190 Building REAL300024450191 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450191' /scratch/stefan/7786230/working/building/REAL300024450191 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450191 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450191/0 /scratch/stefan/7786230/working/building/REAL300024450191 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/44 `/scratch/stefan/7786230/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3CCC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450191/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450191 none CC1C(NC(=O)C2CC3CCC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 8, 8, 26, 42, 80, 80, 80, 80, 80, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 80] 80 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 188 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: REAL300024450191 none CC1C(NC(=O)C2CC3CCC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 67, 67, 67, 80, 80, 80, 80, 80, 80, 64, 64, 64, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 67, 80, 80, 80, 80, 80, 80, 80, 80, 80, 64, 64, 64, 64, 64, 64, 38, 38, 1] 80 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 283 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450191 none CC1C(NC(=O)C2CC3CCC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 11, 24, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 64] 80 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450191 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450191 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450191/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450191 Building REAL300024450192 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450192' /scratch/stefan/7786230/working/building/REAL300024450192 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450192 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450192/0 /scratch/stefan/7786230/working/building/REAL300024450192 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/45 `/scratch/stefan/7786230/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1) `REAL300024450192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450192/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450192 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 60, 60, 60, 60, 60, 1, 1, 37, 37, 37, 37, 37, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 188 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: REAL300024450192 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 162, 62, 62, 62, 60, 60, 60, 60, 60, 57, 24, 57, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 201, 162, 162, 62, 60, 60, 60, 60, 60, 60, 60, 24, 24, 1, 60, 60, 60, 60] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 655 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450192 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 34, 34, 34, 37, 37, 37, 37, 37, 47, 47, 76, 120, 201, 201, 201, 201, 201, 37, 37, 1, 1, 2, 2, 2, 1, 8, 8, 34, 37, 37, 37, 37, 37, 37, 37, 76, 76, 201, 37, 37, 37, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450192 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450192 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450192/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450192 Building REAL300024450193 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450193' /scratch/stefan/7786230/working/building/REAL300024450193 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450193 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450193/0 /scratch/stefan/7786230/working/building/REAL300024450193 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/46 `/scratch/stefan/7786230/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1) `REAL300024450193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450193/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450193 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 76, 76, 76, 76, 76, 1, 1, 12, 12, 27, 27, 27, 27, 27, 12, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 76, 1, 2, 2, 2, 12] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 214 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: REAL300024450193 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 179, 179, 179, 93, 93, 93, 76, 76, 76, 76, 76, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 179, 179, 201, 201, 201, 201, 201, 179, 93, 76, 76, 76, 76, 76, 76, 76, 38, 38, 1, 76, 76, 76, 76, 179] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 577 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450193 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 12, 12, 12, 12, 12, 18, 18, 47, 70, 179, 179, 179, 179, 179, 12, 12, 1, 1, 6, 6, 6, 6, 6, 1, 5, 12, 12, 12, 12, 12, 12, 12, 47, 47, 179, 12, 12, 12, 12, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 397 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450193 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450193 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450193/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450193 Building REAL300024450194 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450194' /scratch/stefan/7786230/working/building/REAL300024450194 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450194 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450194/0 /scratch/stefan/7786230/working/building/REAL300024450194 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/47 `/scratch/stefan/7786230/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=CN=C2N)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450194/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450194 none CC1C(NC(=O)C2=NC=CN=C2N)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 39, 57, 97, 97, 97, 97, 97, 10, 10, 10, 10, 10, 4, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 39, 39, 97] 97 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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, 44, 45]) total number of confs: 252 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: REAL300024450194 none CC1C(NC(=O)C2=NC=CN=C2N)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 96, 96, 96, 97, 97, 97, 97, 97, 97, 71, 71, 71, 67, 37, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 96, 97, 97, 97, 97, 71, 71, 71, 71, 71, 71, 37, 37, 1] 97 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 318 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450194 none CC1C(NC(=O)C2=NC=CN=C2N)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 16, 30, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 71] 97 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450194 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450194 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450194/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450194 Building REAL300024450195 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450195' /scratch/stefan/7786230/working/building/REAL300024450195 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450195 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450195/0 /scratch/stefan/7786230/working/building/REAL300024450195 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/48 `/scratch/stefan/7786230/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450195/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450195 none CC1C(NC(=O)CCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 30, 30, 7, 30, 3, 1, 1, 1, 1, 35, 35, 35, 35, 35, 54, 54, 95, 131, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 30, 7, 7, 3, 3, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 95, 95, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 39] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 567 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: REAL300024450195 none CC1C(NC(=O)CCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 46, 46, 52, 52, 52, 151, 159, 201, 201, 46, 46, 46, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 52, 151, 151, 161, 161, 201, 201, 201, 201, 201, 46, 46, 46, 46, 46, 46, 28, 28, 1] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 815 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450195 none CC1C(NC(=O)CCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 18, 35, 35, 1, 1, 1, 1, 1, 3, 3, 8, 13, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 3, 14, 14, 22, 22, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 8, 8, 46] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450195 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450195 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450195/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450195 Building REAL300024450196 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450196' /scratch/stefan/7786230/working/building/REAL300024450196 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450196 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450196/0 /scratch/stefan/7786230/working/building/REAL300024450196 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/49 `/scratch/stefan/7786230/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1) `REAL300024450196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450196/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450196 none CC1=C(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 33, 88, 88, 88, 88, 88, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 88, 1, 2, 2, 2, 10] 128 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 28 ./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: REAL300024450196 none CC1=C(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 124, 124, 124, 88, 88, 88, 88, 88, 80, 39, 80, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 128, 128, 128, 128, 128, 128, 128, 128, 124, 88, 88, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88, 88, 88, 128] 128 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 402 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450196 none CC1=C(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 17, 17, 51, 76, 128, 128, 128, 128, 128, 10, 10, 1, 1, 2, 2, 2, 2, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 51, 51, 128, 10, 10, 10, 10, 1] 128 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 25, 26] set([6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450196 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450196/1 /scratch/stefan/7786230/working/building/REAL300024450196 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/50 `/scratch/stefan/7786230/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C) `REAL300024450196.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450196/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450196 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 63, 63, 63, 63, 63, 1, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 1, 2, 2, 2, 23, 23, 23] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 52 ./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: REAL300024450196 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 91, 91, 91, 63, 63, 63, 63, 63, 60, 38, 60, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 91, 63, 63, 63, 63, 63, 63, 63, 38, 38, 1, 63, 63, 63, 63, 201, 201, 201] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 466 number of broken/clashed sets: 52 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450196 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 23, 23, 23, 23, 23, 32, 32, 85, 118, 201, 201, 201, 201, 201, 23, 23, 1, 1, 2, 2, 2, 1, 10, 23, 23, 23, 23, 23, 23, 23, 85, 85, 201, 23, 23, 23, 23, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 549 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450196 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450196 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450196/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450196/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450196 Building REAL300024450197 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450197' /scratch/stefan/7786230/working/building/REAL300024450197 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450197 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450197/0 /scratch/stefan/7786230/working/building/REAL300024450197 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/51 `/scratch/stefan/7786230/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450197/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450197 none CC1C(NC(=O)CC2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 24, 24, 5, 24, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 49, 49, 81, 123, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 81, 81, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 535 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: REAL300024450197 none CC1C(NC(=O)CC2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 71, 71, 71, 190, 201, 201, 201, 201, 201, 58, 58, 58, 56, 28, 56, 12, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 71, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 28, 28, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 772 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450197 none CC1C(NC(=O)CC2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 4, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 9, 9, 58] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 205 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450197 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450197 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450197/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450197 Building REAL300024450198 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450198' /scratch/stefan/7786230/working/building/REAL300024450198 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450198 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450198/0 /scratch/stefan/7786230/working/building/REAL300024450198 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/52 `/scratch/stefan/7786230/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450198/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450198 none CCCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 104, 100, 46, 46, 46, 39, 39, 39, 39, 39, 39, 23, 39, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 201, 201, 108, 108, 100, 100, 46, 39, 39, 39, 39, 39, 39, 39, 23, 23, 1, 39, 39, 39, 39] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 853 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450198 none CCCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 19, 14, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 39, 39, 39, 39, 39, 1, 1, 33, 33, 33, 33, 33, 33, 33, 19, 19, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450198 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450198 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450198/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450198 Building REAL300024450199 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450199' /scratch/stefan/7786230/working/building/REAL300024450199 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450199 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450199/0 /scratch/stefan/7786230/working/building/REAL300024450199 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/53 `/scratch/stefan/7786230/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450199/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450199 none CC1C(NC(=O)CC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 23, 23, 4, 23, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 46, 46, 87, 131, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 23, 4, 4, 1, 1, 32, 32, 32, 32, 32, 32, 87, 87, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 554 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: REAL300024450199 none CC1C(NC(=O)CC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 94, 94, 94, 192, 201, 201, 201, 201, 71, 71, 71, 71, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 94, 192, 192, 201, 201, 71, 71, 71, 71, 71, 71, 28, 28, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 753 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450199 none CC1C(NC(=O)CC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 19, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 19, 19, 32, 32, 1, 1, 1, 1, 1, 1, 10, 10, 71] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450199 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450199 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450199/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450199 Building REAL300024450200 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450200' /scratch/stefan/7786230/working/building/REAL300024450200 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450200 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450200/0 /scratch/stefan/7786230/working/building/REAL300024450200 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/54 `/scratch/stefan/7786230/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1) `REAL300024450200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450200/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450200 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 30, 127, 127, 127, 127, 127, 1, 1, 9, 10, 10, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 127, 1, 2, 2, 2, 10] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 285 number of broken/clashed sets: 20 ./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: REAL300024450200 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 196, 177, 177, 177, 127, 127, 127, 127, 127, 115, 30, 115, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 196, 196, 196, 201, 201, 201, 201, 201, 177, 127, 127, 127, 127, 127, 127, 127, 30, 30, 1, 127, 127, 127, 127, 196] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450200 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 18, 18, 50, 87, 196, 196, 196, 196, 196, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 50, 50, 196, 10, 10, 10, 10, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 436 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450200 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450200 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450200/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450200 Building REAL300024450201 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450201' /scratch/stefan/7786230/working/building/REAL300024450201 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450201 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450201/0 /scratch/stefan/7786230/working/building/REAL300024450201 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/55 `/scratch/stefan/7786230/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450201/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450201 none CC1C(NC(=O)CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 42, 42, 82, 132, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 82, 82, 201] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 548 number of broken/clashed sets: 6 ./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: REAL300024450201 none CC1C(NC(=O)CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 53, 53, 61, 61, 61, 192, 201, 201, 201, 201, 53, 53, 53, 51, 24, 51, 12, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 61, 192, 192, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 53, 53, 53, 24, 24, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 718 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450201 none CC1C(NC(=O)CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 9, 17, 53, 53, 53, 53, 53, 2, 2, 2, 1, 1, 4, 16, 16, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 9, 9, 53] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450201 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450201 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450201/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450201 Building REAL300024450202 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450202' /scratch/stefan/7786230/working/building/REAL300024450202 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450202 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450202/0 /scratch/stefan/7786230/working/building/REAL300024450202 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/56 `/scratch/stefan/7786230/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450202/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450202 none CC1C(NC(=O)C2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 57, 107, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 57, 57, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 448 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: REAL300024450202 none CC1C(NC(=O)C2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [111, 111, 111, 111, 119, 119, 119, 201, 201, 201, 201, 111, 111, 111, 111, 54, 111, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 119, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111, 54, 54, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 627 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450202 none CC1C(NC(=O)C2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 35, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 111] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450202 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450202 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450202/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450202 Building REAL300024450203 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450203' /scratch/stefan/7786230/working/building/REAL300024450203 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450203 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450203/0 /scratch/stefan/7786230/working/building/REAL300024450203 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/57 `/scratch/stefan/7786230/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450203/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450203 none CC1C(NC(=O)CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 20, 20, 6, 20, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 42, 42, 89, 130, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 20, 6, 6, 1, 1, 1, 30, 30, 30, 30, 30, 30, 89, 89, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 554 number of broken/clashed sets: 6 ./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: REAL300024450203 none CC1C(NC(=O)CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [86, 86, 86, 86, 116, 116, 116, 193, 201, 201, 201, 201, 86, 86, 86, 82, 30, 82, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 116, 193, 193, 201, 201, 201, 86, 86, 86, 86, 86, 86, 30, 30, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 791 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450203 none CC1C(NC(=O)CC2=NNC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 18, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 18, 86, 86, 86, 86, 86, 2, 2, 2, 1, 1, 5, 18, 18, 30, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 86] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450203 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450203 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450203/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450203 Building REAL300024450204 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450204' /scratch/stefan/7786230/working/building/REAL300024450204 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450204 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450204/0 /scratch/stefan/7786230/working/building/REAL300024450204 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/58 `/scratch/stefan/7786230/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=NC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450204/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450204 none CC1C(NC(=O)C2=CC=NC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 63, 121, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 1, 1, 1, 14, 14, 14, 14, 14, 14, 63, 63, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 467 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: REAL300024450204 none CC1C(NC(=O)C2=CC=NC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [135, 135, 135, 135, 158, 158, 158, 201, 201, 201, 201, 201, 201, 135, 135, 135, 132, 53, 132, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 158, 201, 201, 201, 135, 135, 135, 135, 135, 135, 53, 53, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 571 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450204 none CC1C(NC(=O)C2=CC=NC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 13, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 13, 41, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 3, 14, 14, 14, 1, 1, 1, 1, 1, 1, 13, 13, 135] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450204 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450204 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450204/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450204 Building REAL300024450205 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450205' /scratch/stefan/7786230/working/building/REAL300024450205 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450205 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450205/0 /scratch/stefan/7786230/working/building/REAL300024450205 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/59 `/scratch/stefan/7786230/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=NN1C) `REAL300024450205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450205/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450205 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 34, 106, 106, 106, 106, 106, 1, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 106, 1, 2, 2, 2, 19, 19, 19] 193 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 39 ./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: REAL300024450205 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [193, 193, 142, 142, 142, 106, 106, 106, 106, 106, 95, 41, 95, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 193, 193, 193, 193, 193, 193, 193, 142, 106, 106, 106, 106, 106, 106, 106, 41, 41, 1, 106, 106, 106, 106, 193, 193, 193] 193 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 556 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450205 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 27, 27, 81, 124, 193, 193, 193, 193, 193, 19, 19, 1, 1, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 19, 19, 19, 81, 81, 193, 19, 19, 19, 19, 2, 2, 2] 193 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 517 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450205 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450205 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450205/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450205 Building REAL300024450206 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450206' /scratch/stefan/7786230/working/building/REAL300024450206 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450206 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450206/0 /scratch/stefan/7786230/working/building/REAL300024450206 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/60 `/scratch/stefan/7786230/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450206/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450206 none CC1=CC=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 30, 85, 85, 85, 85, 85, 1, 1, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 85, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 38 ./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: REAL300024450206 none CC1=CC=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 88, 88, 88, 85, 85, 85, 85, 85, 79, 38, 79, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 88, 85, 85, 85, 85, 85, 85, 85, 38, 38, 1, 85, 85, 85, 85] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 448 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450206 none CC1=CC=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 15, 15, 15, 15, 15, 21, 21, 76, 125, 201, 201, 201, 201, 201, 15, 15, 2, 2, 2, 1, 1, 1, 10, 15, 15, 15, 15, 15, 15, 15, 76, 76, 201, 15, 15, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 512 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450206 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450206 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450206/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450206 Building REAL300024450207 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450207' /scratch/stefan/7786230/working/building/REAL300024450207 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450207 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450207/0 /scratch/stefan/7786230/working/building/REAL300024450207 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/61 `/scratch/stefan/7786230/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450207/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450207 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 65, 65, 65, 65, 65, 1, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 65, 1, 2, 2, 2, 12] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 22 ./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: REAL300024450207 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 67, 67, 67, 65, 65, 65, 65, 65, 63, 34, 63, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 67, 65, 65, 65, 65, 65, 65, 65, 34, 34, 1, 65, 65, 65, 65, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450207 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 12, 12, 12, 12, 12, 18, 18, 46, 93, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 46, 46, 201, 12, 12, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 425 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450207 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450207 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450207/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450207 Building REAL300024450208 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450208' /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450208 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450208/0 /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/62 `/scratch/stefan/7786230/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CN(C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450208/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2CN(C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 29, 29, 78, 106, 155, 155, 155, 155, 155, 20, 20, 20, 20, 20, 10, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 78, 78, 155] 155 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 448 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: REAL300024450208 none CC1C(NC(=O)C2CN(C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 110, 110, 110, 155, 155, 155, 155, 155, 155, 82, 82, 82, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 110, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 82, 82, 82, 82, 82, 82, 39, 39, 1] 155 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 516 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2CN(C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 3, 16, 29, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 16, 16, 82] 155 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450208/1 /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/63 `/scratch/stefan/7786230/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C[N@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450208.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450208/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2C[N@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 24, 24, 48, 61, 91, 91, 91, 91, 91, 16, 16, 16, 16, 16, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 48, 48, 91] 91 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 43, 41, 36, 42] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 275 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: REAL300024450208 none CC1C(NC(=O)C2C[N@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 78, 78, 78, 91, 91, 91, 91, 91, 91, 91, 54, 54, 54, 54, 35, 54, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 78, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 54, 54, 54, 54, 54, 54, 35, 35, 1] 91 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 332 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2C[N@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 9, 17, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 9, 9, 54] 91 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450208/2 /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/64 `/scratch/stefan/7786230/working/3D/64' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C[N@@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450208.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450208/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2C[N@@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 13 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: REAL300024450208 none CC1C(NC(=O)C2C[N@@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 5 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 6 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450208 none CC1C(NC(=O)C2C[N@@H+](C)CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5] 5 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450208 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450208 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450208/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450208/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450208/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450208 Building REAL300024450209 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450209' /scratch/stefan/7786230/working/building/REAL300024450209 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450209 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450209/0 /scratch/stefan/7786230/working/building/REAL300024450209 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/65 `/scratch/stefan/7786230/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450209/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450209 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 27, 74, 74, 74, 74, 74, 1, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 74, 1, 2, 2, 2] 144 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 31 ./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: REAL300024450209 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 144, 144, 144, 112, 112, 112, 74, 74, 74, 74, 74, 68, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 144, 144, 144, 144, 144, 144, 144, 112, 74, 74, 74, 74, 74, 74, 74, 36, 36, 1, 74, 74, 74, 74] 144 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450209 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 21, 21, 60, 87, 144, 144, 144, 144, 144, 15, 15, 1, 2, 2, 2, 2, 2, 2, 7, 15, 15, 15, 15, 15, 15, 15, 60, 60, 144, 15, 15, 15, 15] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 391 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450209 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450209 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450209/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450209 Building REAL300024450210 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450210' /scratch/stefan/7786230/working/building/REAL300024450210 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450210 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450210/0 /scratch/stefan/7786230/working/building/REAL300024450210 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/66 `/scratch/stefan/7786230/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450210/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450210 none CC1C(NC(=O)CCC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 54, 54, 73, 73, 73, 165, 201, 201, 201, 201, 54, 54, 54, 54, 39, 54, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 73, 165, 165, 201, 201, 54, 54, 54, 54, 54, 54, 39, 39, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 867 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450210 none CC1C(NC(=O)CCC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 21, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 9, 15, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 3, 18, 18, 25, 25, 1, 1, 1, 1, 1, 1, 9, 9, 54] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450210 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450210 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450210/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450210 Building REAL300024450211 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450211' /scratch/stefan/7786230/working/building/REAL300024450211 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450211 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450211/0 /scratch/stefan/7786230/working/building/REAL300024450211 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/67 `/scratch/stefan/7786230/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450211/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450211 none C=CCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 157, 145, 156, 63, 63, 63, 57, 57, 57, 57, 57, 54, 25, 54, 11, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 150, 152, 157, 157, 156, 156, 63, 57, 57, 57, 57, 57, 57, 57, 25, 25, 1, 57, 57, 57, 57] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 895 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450211 none C=CCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 32, 17, 12, 10, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 57, 57, 57, 57, 57, 1, 1, 39, 39, 39, 32, 32, 11, 11, 12, 12, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 57, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 258 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450211 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450211 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450211/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450211 Building REAL300024450212 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450212' /scratch/stefan/7786230/working/building/REAL300024450212 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450212 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450212/0 /scratch/stefan/7786230/working/building/REAL300024450212 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/68 `/scratch/stefan/7786230/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450212/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450212 none CC1C(NC(=O)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 27, 27, 6, 27, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 47, 47, 105, 145, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 105, 105, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 39, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 574 number of broken/clashed sets: 23 ./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: REAL300024450212 none CC1C(NC(=O)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 81, 81, 81, 155, 201, 201, 201, 75, 75, 75, 68, 26, 68, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 81, 155, 155, 201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75, 75, 75, 26, 26, 1] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 788 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450212 none CC1C(NC(=O)CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 12, 23, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 3, 15, 15, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 12, 12, 75] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450212 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450212 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450212/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450212 Building REAL300024450213 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450213' /scratch/stefan/7786230/working/building/REAL300024450213 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450213 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450213/0 /scratch/stefan/7786230/working/building/REAL300024450213 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/69 `/scratch/stefan/7786230/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450213/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450213 none CC1C(NC(=O)C2=CC=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 39, 39, 91, 124, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 12, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 91, 91, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 558 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: REAL300024450213 none CC1C(NC(=O)C2=CC=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 91, 91, 91, 201, 201, 201, 201, 201, 201, 69, 69, 69, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 91, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 38, 38, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 471 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450213 none CC1C(NC(=O)C2=CC=CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 11, 19, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 6, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 11, 11, 69] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450213 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450213 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450213/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450213 Building REAL300024450214 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450214' /scratch/stefan/7786230/working/building/REAL300024450214 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450214 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450214/0 /scratch/stefan/7786230/working/building/REAL300024450214 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/70 `/scratch/stefan/7786230/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C(C)(C)C2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450214/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450214 none CC1C(NC(=O)C2C(C)(C)C2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 46, 105, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 46, 46, 201] 201 rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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, 52, 53, 54]) total number of confs: 443 number of broken/clashed sets: 200 ./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: REAL300024450214 none CC1C(NC(=O)C2C(C)(C)C2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 125, 125, 125, 201, 201, 201, 201, 201, 201, 119, 119, 119, 113, 54, 113, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 54, 54, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 657 number of broken/clashed sets: 200 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450214 none CC1C(NC(=O)C2C(C)(C)C2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 33, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 119] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450214 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450214 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450214/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450214 Building REAL300024450215 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450215' /scratch/stefan/7786230/working/building/REAL300024450215 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450215 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450215/0 /scratch/stefan/7786230/working/building/REAL300024450215 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/71 `/scratch/stefan/7786230/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1) `REAL300024450215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450215/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450215 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 39, 124, 124, 124, 124, 124, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 124, 1, 2, 2, 2, 15] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 22 ./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: REAL300024450215 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 175, 175, 175, 124, 124, 124, 124, 124, 118, 50, 118, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201, 201, 201, 201, 175, 124, 124, 124, 124, 124, 124, 124, 50, 50, 1, 124, 124, 124, 124, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 608 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450215 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 15, 15, 15, 15, 15, 22, 22, 65, 130, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 15, 15, 15, 15, 65, 65, 201, 15, 15, 15, 15, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 479 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450215 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450215 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450215/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450215 Building REAL300024450216 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450216' /scratch/stefan/7786230/working/building/REAL300024450216 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450216 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450216/0 /scratch/stefan/7786230/working/building/REAL300024450216 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/72 `/scratch/stefan/7786230/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450216/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450216 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8, 8, 8, 9, 9, 9, 9, 9] 9 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 23 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: REAL300024450216 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 7, 8, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 2, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 7, 7, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [1, 44, 45, 46, 47, 48, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 31 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450216 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 8, 8, 8, 8, 1, 1, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 2, 2, 2, 5, 5, 5, 5, 5] 9 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 36, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450216 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450216 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450216/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450216 Building REAL300024450217 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450217' /scratch/stefan/7786230/working/building/REAL300024450217 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450217 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450217/0 /scratch/stefan/7786230/working/building/REAL300024450217 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/73 `/scratch/stefan/7786230/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450217/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450217 none CC1C(NC(=O)C2C3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 24, 24, 71, 117, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 71, 71, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 486 number of broken/clashed sets: 36 ./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: REAL300024450217 none CC1C(NC(=O)C2C3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 80, 80, 80, 201, 201, 201, 201, 201, 77, 77, 77, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 77, 40, 40, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 614 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450217 none CC1C(NC(=O)C2C3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 13, 24, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 13, 13, 77] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450217 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450217 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450217/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450217 Building REAL300024450218 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450218' /scratch/stefan/7786230/working/building/REAL300024450218 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450218 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450218/0 /scratch/stefan/7786230/working/building/REAL300024450218 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/74 `/scratch/stefan/7786230/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(C#N)=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450218/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450218 none CC1C(NC(=O)C2=CC(C#N)=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 18, 22, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 18, 18, 34] 34 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 10 ./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: REAL300024450218 none CC1C(NC(=O)C2=CC(C#N)=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 26, 26, 27, 27, 27, 34, 34, 34, 34, 34, 34, 26, 26, 26, 26, 21, 26, 13, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 27, 34, 34, 34, 26, 26, 26, 26, 26, 26, 21, 21, 1] 34 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450218 none CC1C(NC(=O)C2=CC(C#N)=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 8, 11, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 3, 6, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 26] 34 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450218 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450218 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450218/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450218 Building REAL300024450219 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450219' /scratch/stefan/7786230/working/building/REAL300024450219 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450219 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450219/0 /scratch/stefan/7786230/working/building/REAL300024450219 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/75 `/scratch/stefan/7786230/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450219/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450219 none CC1=CSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 30, 87, 87, 87, 87, 87, 1, 1, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 170 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: REAL300024450219 none CC1=CSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 98, 98, 98, 87, 87, 87, 87, 87, 83, 44, 83, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 98, 87, 87, 87, 87, 87, 87, 87, 44, 44, 1, 87, 87, 87, 87] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 479 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450219 none CC1=CSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 14, 14, 14, 14, 14, 22, 22, 59, 105, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 59, 59, 201, 14, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 470 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450219 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450219 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450219/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450219 Building REAL300024450220 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450220' /scratch/stefan/7786230/working/building/REAL300024450220 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450220 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450220/0 /scratch/stefan/7786230/working/building/REAL300024450220 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/76 `/scratch/stefan/7786230/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450220/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450220 none CC1C(NC(=O)CCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 10, 41, 6, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 63, 63, 94, 128, 201, 201, 201, 201, 201, 41, 41, 41, 41, 41, 41, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 94, 94, 201] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 572 number of broken/clashed sets: 25 ./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: REAL300024450220 none CC1C(NC(=O)CCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 35, 35, 35, 35, 129, 139, 201, 201, 201, 35, 35, 35, 35, 23, 35, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 129, 129, 163, 163, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 35, 23, 23, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 925 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450220 none CC1C(NC(=O)CCC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 2, 10, 14, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 6, 9, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 2, 10, 10, 18, 18, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 6, 6, 35] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450220 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450220 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450220/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450220 Building REAL300024450221 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450221' /scratch/stefan/7786230/working/building/REAL300024450221 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450221 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450221/0 /scratch/stefan/7786230/working/building/REAL300024450221 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/77 `/scratch/stefan/7786230/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450221/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450221 none CC1=CC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 90, 90, 90, 90, 90, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 90, 1, 2, 2, 2] 155 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 29 ./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: REAL300024450221 none CC1=CC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 155, 94, 94, 94, 90, 90, 90, 90, 90, 82, 41, 82, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 155, 155, 155, 155, 155, 155, 155, 155, 94, 90, 90, 90, 90, 90, 90, 90, 41, 41, 1, 90, 90, 90, 90] 155 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 403 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450221 none CC1=CC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 20, 20, 63, 98, 155, 155, 155, 155, 155, 14, 14, 1, 2, 2, 2, 1, 2, 2, 2, 8, 14, 14, 14, 14, 14, 14, 14, 63, 63, 155, 14, 14, 14, 14] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 402 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450221 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450221 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450221/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450221 Building REAL300024450222 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450222' /scratch/stefan/7786230/working/building/REAL300024450222 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450222 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450222/0 /scratch/stefan/7786230/working/building/REAL300024450222 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/78 `/scratch/stefan/7786230/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450222/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450222 none CC1C(NC(=O)CCC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 15, 15, 8, 15, 5, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 27, 27, 64, 102, 161, 161, 161, 161, 161, 21, 21, 21, 21, 21, 15, 8, 8, 5, 5, 1, 1, 21, 21, 21, 21, 21, 21, 64, 64, 161] 161 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 442 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: REAL300024450222 none CC1C(NC(=O)CCC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 86, 86, 86, 155, 161, 161, 161, 161, 161, 55, 55, 55, 54, 35, 54, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 86, 155, 155, 161, 161, 161, 161, 55, 55, 55, 55, 55, 55, 35, 35, 1] 161 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 624 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450222 none CC1C(NC(=O)CCC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 15, 19, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 10, 18, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 6, 15, 15, 19, 19, 21, 21, 1, 1, 1, 1, 1, 1, 10, 10, 55] 161 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450222 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450222/1 /scratch/stefan/7786230/working/building/REAL300024450222 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/79 `/scratch/stefan/7786230/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450222.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450222/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450222 none CC1C(NC(=O)CCC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 7 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: REAL300024450222 none CC1C(NC(=O)CCC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 2 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 3 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450222 none CC1C(NC(=O)CCC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450222 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450222 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450222/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450222/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450222 Building REAL300024450223 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450223' /scratch/stefan/7786230/working/building/REAL300024450223 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450223 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450223/0 /scratch/stefan/7786230/working/building/REAL300024450223 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/80 `/scratch/stefan/7786230/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450223/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450223 none CC1=CC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 36, 106, 106, 106, 106, 106, 1, 1, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 106, 1, 2, 2, 2] 177 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 34 ./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: REAL300024450223 none CC1=CC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 114, 114, 114, 106, 106, 106, 106, 106, 95, 43, 95, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 177, 177, 177, 177, 177, 177, 114, 106, 106, 106, 106, 106, 106, 106, 43, 43, 1, 106, 106, 106, 106] 177 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 465 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450223 none CC1=CC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 13, 13, 22, 22, 73, 113, 177, 177, 177, 177, 177, 13, 13, 2, 2, 2, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 73, 73, 177, 13, 13, 13, 13] 177 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 464 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450223 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450223 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450223/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450223 Building REAL300024450224 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450224' /scratch/stefan/7786230/working/building/REAL300024450224 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450224 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450224/0 /scratch/stefan/7786230/working/building/REAL300024450224 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/81 `/scratch/stefan/7786230/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450224/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450224 none CC=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 110, 201, 110, 110, 92, 92, 92, 92, 92, 89, 48, 89, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 110, 92, 92, 92, 92, 92, 92, 92, 48, 48, 1, 92, 92, 92, 92] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 655 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450224 none CC=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 4, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 28, 92, 92, 92, 92, 92, 1, 1, 16, 16, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 92, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450224 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450224 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450224/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450224 Building REAL300024450225 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450225' /scratch/stefan/7786230/working/building/REAL300024450225 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450225 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450225/0 /scratch/stefan/7786230/working/building/REAL300024450225 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/82 `/scratch/stefan/7786230/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450225/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450225 none CC1C(NC(=O)CCC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 41, 41, 8, 41, 5, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 65, 65, 96, 122, 201, 201, 201, 201, 201, 45, 45, 45, 45, 45, 41, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 96, 96, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 567 number of broken/clashed sets: 18 ./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: REAL300024450225 none CC1C(NC(=O)CCC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 35, 38, 38, 38, 134, 156, 201, 201, 201, 201, 35, 35, 35, 35, 23, 35, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 38, 134, 134, 172, 172, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 35, 23, 23, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 902 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450225 none CC1C(NC(=O)CCC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 17, 45, 45, 45, 45, 1, 1, 1, 1, 1, 3, 3, 6, 9, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 3, 13, 13, 21, 21, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 6, 6, 35] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 233 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450225 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450225 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450225/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450225 Building REAL300024450226 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450226' /scratch/stefan/7786230/working/building/REAL300024450226 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450226 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450226/0 /scratch/stefan/7786230/working/building/REAL300024450226 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/83 `/scratch/stefan/7786230/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450226/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450226 none CC1C(NC(=O)CCC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 27, 27, 6, 27, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 51, 51, 94, 131, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 27, 6, 6, 2, 2, 1, 1, 1, 32, 32, 32, 32, 32, 32, 94, 94, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 575 number of broken/clashed sets: 24 ./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: REAL300024450226 none CC1C(NC(=O)CCC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 47, 47, 47, 130, 134, 201, 201, 201, 201, 41, 41, 41, 41, 25, 41, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 47, 130, 130, 134, 134, 201, 201, 201, 41, 41, 41, 41, 41, 41, 25, 25, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 652 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450226 none CC1C(NC(=O)CCC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 17, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 8, 12, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 3, 12, 12, 17, 17, 32, 32, 32, 1, 1, 1, 1, 1, 1, 8, 8, 41] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450226 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450226 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450226/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450226 Building REAL300024450227 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450227' /scratch/stefan/7786230/working/building/REAL300024450227 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450227 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450227/0 /scratch/stefan/7786230/working/building/REAL300024450227 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/84 `/scratch/stefan/7786230/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(F)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450227/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450227 none CC1C(NC(=O)C2CC(F)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 23, 23, 65, 113, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 11, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 65, 65, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 45]) total number of confs: 464 number of broken/clashed sets: 22 ./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: REAL300024450227 none CC1C(NC(=O)C2CC(F)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 96, 96, 99, 99, 99, 201, 201, 201, 201, 201, 96, 96, 96, 94, 46, 94, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 99, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 46, 46, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 631 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450227 none CC1C(NC(=O)C2CC(F)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 13, 29, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 13, 13, 96] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450227 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450227 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450227/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450227 Building REAL300024450228 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450228' /scratch/stefan/7786230/working/building/REAL300024450228 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450228 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450228/0 /scratch/stefan/7786230/working/building/REAL300024450228 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/85 `/scratch/stefan/7786230/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450228/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450228 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 64, 64, 64, 64, 64, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 64, 1, 2, 2, 2, 24, 24] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 40 ./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: REAL300024450228 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 76, 76, 76, 64, 64, 64, 64, 64, 60, 38, 60, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 76, 64, 64, 64, 64, 64, 64, 64, 38, 38, 1, 64, 64, 64, 64, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 629 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450228 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 11, 24, 24, 24, 24, 24, 34, 34, 86, 123, 201, 201, 201, 201, 201, 24, 24, 1, 2, 2, 2, 1, 1, 1, 1, 11, 24, 24, 24, 24, 24, 24, 24, 86, 86, 201, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 48, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450228 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450228 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450228/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450228 Building REAL300024450229 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450229' /scratch/stefan/7786230/working/building/REAL300024450229 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450229 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450229/0 /scratch/stefan/7786230/working/building/REAL300024450229 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/86 `/scratch/stefan/7786230/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCCC1) `REAL300024450229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450229/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450229 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 87, 87, 70, 70, 70, 70, 70, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 87, 70, 70, 70, 70, 70, 70, 70, 38, 38, 1, 70, 70, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 625 number of broken/clashed sets: 42 ./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: REAL300024450229 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 31, 31, 31, 31, 31, 42, 42, 95, 130, 201, 201, 201, 201, 201, 31, 31, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 31, 31, 31, 31, 31, 31, 95, 95, 201, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 45, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([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]) total number of confs: 559 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450229 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 70, 70, 70, 70, 70, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 70, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450229 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450229 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450229/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450229 Building REAL300024450230 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450230' /scratch/stefan/7786230/working/building/REAL300024450230 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450230 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450230/0 /scratch/stefan/7786230/working/building/REAL300024450230 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/87 `/scratch/stefan/7786230/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450230/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450230 none CC1C(NC(=O)CC2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 26, 26, 6, 26, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 51, 51, 87, 125, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 87, 87, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 548 number of broken/clashed sets: 6 ./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: REAL300024450230 none CC1C(NC(=O)CC2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 80, 80, 80, 175, 201, 201, 201, 201, 201, 76, 76, 76, 74, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 80, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 28, 28, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 738 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450230 none CC1C(NC(=O)CC2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 11, 20, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 4, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 11, 11, 76] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 241 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450230 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450230 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450230/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450230 Building REAL300024450231 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450231' /scratch/stefan/7786230/working/building/REAL300024450231 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450231 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450231/0 /scratch/stefan/7786230/working/building/REAL300024450231 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/88 `/scratch/stefan/7786230/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1) `REAL300024450231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450231/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450231 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 26, 92, 92, 92, 92, 92, 1, 1, 31, 31, 31, 31, 31, 31, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 92, 1, 2, 2, 2, 31] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 225 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: REAL300024450231 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 179, 100, 100, 100, 92, 92, 92, 92, 92, 88, 27, 88, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 179, 179, 100, 92, 92, 92, 92, 92, 92, 92, 27, 27, 1, 92, 92, 92, 92, 201] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 698 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450231 none CC1=CC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 29, 29, 29, 31, 31, 31, 31, 31, 46, 46, 84, 123, 201, 201, 201, 201, 201, 31, 31, 1, 1, 2, 2, 2, 1, 8, 8, 29, 31, 31, 31, 31, 31, 31, 31, 84, 84, 201, 31, 31, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 48, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 534 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450231 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450231/1 /scratch/stefan/7786230/working/building/REAL300024450231 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/89 `/scratch/stefan/7786230/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450231/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450231 none CC1=NNC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 32, 32, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 76, 76, 76, 76, 76, 1, 1, 32, 32, 32, 32, 32, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 76, 1, 2, 2, 2, 32] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 210 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: REAL300024450231 none CC1=NNC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 200, 108, 108, 108, 76, 76, 76, 76, 76, 74, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 200, 200, 108, 76, 76, 76, 76, 76, 76, 76, 28, 28, 1, 76, 76, 76, 76, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 769 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450231 none CC1=NNC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 22, 22, 22, 32, 32, 32, 32, 32, 47, 47, 87, 129, 201, 201, 201, 201, 201, 32, 32, 1, 2, 2, 2, 1, 6, 6, 22, 32, 32, 32, 32, 32, 32, 32, 87, 87, 201, 32, 32, 32, 32, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450231 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450231 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450231/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450231/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450231 Building REAL300024450232 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450232' /scratch/stefan/7786230/working/building/REAL300024450232 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450232 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450232/0 /scratch/stefan/7786230/working/building/REAL300024450232 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/90 `/scratch/stefan/7786230/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450232/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450232 none CC1C(NC(=O)C=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 78, 119, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 78, 78, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 513 number of broken/clashed sets: 38 ./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: REAL300024450232 none CC1C(NC(=O)C=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [90, 90, 90, 90, 97, 97, 97, 201, 201, 201, 201, 90, 90, 90, 85, 40, 85, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 97, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 90, 90, 90, 40, 40, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 623 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450232 none CC1C(NC(=O)C=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 14, 27, 90, 90, 90, 90, 90, 2, 2, 2, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 14, 14, 90] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450232 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450232 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450232/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450232 Building REAL300024450233 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450233' /scratch/stefan/7786230/working/building/REAL300024450233 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450233 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450233/0 /scratch/stefan/7786230/working/building/REAL300024450233 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/91 `/scratch/stefan/7786230/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450233/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450233 none CC1C(NC(=O)C2=CN=CC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 15, 15, 45, 94, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 45, 45, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 421 number of broken/clashed sets: 22 ./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: REAL300024450233 none CC1C(NC(=O)C2=CN=CC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 75, 75, 75, 201, 201, 201, 201, 201, 201, 72, 72, 72, 70, 39, 70, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 75, 201, 201, 201, 72, 72, 72, 72, 72, 72, 39, 39, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 420 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450233 none CC1C(NC(=O)C2=CN=CC(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 11, 27, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 5, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 72] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450233 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450233 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450233/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450233 Building REAL300024450234 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450234' /scratch/stefan/7786230/working/building/REAL300024450234 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450234 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450234/0 /scratch/stefan/7786230/working/building/REAL300024450234 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/92 `/scratch/stefan/7786230/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC) `REAL300024450234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450234/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450234 none CCC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [158, 104, 104, 71, 71, 71, 53, 53, 53, 53, 53, 51, 23, 51, 12, 1, 1, 1, 1, 1, 1, 1, 53, 53, 104, 139, 158, 158, 158, 158, 158, 104, 71, 53, 53, 53, 53, 53, 53, 53, 23, 23, 1, 53, 53, 53, 53, 139, 139, 139, 139, 139] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 893 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450234 none CCC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 53, 53, 53, 53, 53, 1, 1, 12, 17, 19, 19, 19, 19, 19, 12, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 53, 1, 2, 2, 2, 17, 17, 17, 17, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450234 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450234 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450234/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450234 Building REAL300024450235 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450235' /scratch/stefan/7786230/working/building/REAL300024450235 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450235 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450235/0 /scratch/stefan/7786230/working/building/REAL300024450235 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/93 `/scratch/stefan/7786230/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)NC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450235/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450235 none CC1C(NC(=O)C2=CC(=O)NC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 40, 98, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 40, 40, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 402 number of broken/clashed sets: 29 ./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: REAL300024450235 none CC1C(NC(=O)C2=CC(=O)NC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [100, 100, 100, 100, 103, 103, 103, 201, 201, 201, 201, 201, 201, 100, 100, 100, 99, 53, 99, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 103, 201, 201, 201, 201, 100, 100, 100, 100, 100, 100, 53, 53, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 477 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450235 none CC1C(NC(=O)C2=CC(=O)NC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 14, 39, 100, 100, 100, 100, 100, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 14, 100] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450235 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450235 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450235/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450235 Building REAL300024450236 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450236' /scratch/stefan/7786230/working/building/REAL300024450236 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450236 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450236/0 /scratch/stefan/7786230/working/building/REAL300024450236 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/94 `/scratch/stefan/7786230/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450236/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450236 none CC(C)=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 201, 146, 146, 137, 137, 137, 137, 137, 136, 60, 136, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 201, 146, 137, 137, 137, 137, 137, 137, 137, 60, 60, 1, 137, 137, 137, 137] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 659 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450236 none CC(C)=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 4, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 39, 137, 137, 137, 137, 137, 1, 1, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 137, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 242 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450236 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450236 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450236/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450236 Building REAL300024450237 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450237' /scratch/stefan/7786230/working/building/REAL300024450237 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450237 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450237/0 /scratch/stefan/7786230/working/building/REAL300024450237 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/95 `/scratch/stefan/7786230/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450237/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450237 none CC1C(NC(=O)C2CCNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 22, 22, 73, 110, 175, 175, 175, 175, 175, 17, 17, 17, 17, 17, 12, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 73, 73, 175] 175 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 446 number of broken/clashed sets: 35 ./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: REAL300024450237 none CC1C(NC(=O)C2CCNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 79, 79, 79, 175, 175, 175, 175, 175, 175, 76, 76, 76, 73, 38, 73, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 79, 175, 175, 175, 175, 175, 175, 175, 175, 76, 76, 76, 76, 76, 76, 38, 38, 1] 175 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 545 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450237 none CC1C(NC(=O)C2CCNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 12, 23, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 12, 12, 76] 175 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450237 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450237 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450237/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450237 Building REAL300024450238 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450238' /scratch/stefan/7786230/working/building/REAL300024450238 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450238 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450238/0 /scratch/stefan/7786230/working/building/REAL300024450238 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/96 `/scratch/stefan/7786230/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450238/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450238 none CC1C(NC(=O)C2=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 28, 28, 80, 127, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 80, 80, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 490 number of broken/clashed sets: 29 ./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: REAL300024450238 none CC1C(NC(=O)C2=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [194, 194, 194, 194, 198, 198, 198, 201, 201, 201, 201, 194, 194, 194, 185, 66, 185, 13, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 198, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 194, 194, 194, 66, 66, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450238 none CC1C(NC(=O)C2=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 16, 1, 1, 1, 1, 1, 4, 4, 17, 54, 194, 194, 194, 194, 194, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 194] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 325 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450238 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450238 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450238/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450238 Building REAL300024450239 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450239' /scratch/stefan/7786230/working/building/REAL300024450239 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450239 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450239/0 /scratch/stefan/7786230/working/building/REAL300024450239 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/97 `/scratch/stefan/7786230/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450239/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450239 none CC1C(NC(=O)C(F)=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 28, 28, 92, 135, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 92, 92, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 532 number of broken/clashed sets: 36 ./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: REAL300024450239 none CC1C(NC(=O)C(F)=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 103, 103, 103, 117, 117, 117, 201, 201, 201, 201, 201, 201, 103, 103, 103, 95, 42, 95, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 117, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 103, 42, 42, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 625 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450239 none CC1C(NC(=O)C(F)=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 14, 27, 103, 103, 103, 103, 103, 2, 2, 2, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 14, 14, 103] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450239 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450239 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450239/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450239 Building REAL300024450240 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450240' /scratch/stefan/7786230/working/building/REAL300024450240 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450240 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450240/0 /scratch/stefan/7786230/working/building/REAL300024450240 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/98 `/scratch/stefan/7786230/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450240/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450240 none CC1C(NC(=O)C2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 53, 108, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 53, 53, 201] 201 rigid atoms, others: [32, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 443 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: REAL300024450240 none CC1C(NC(=O)C2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 121, 121, 121, 133, 133, 133, 201, 201, 201, 201, 201, 121, 121, 121, 119, 50, 119, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 133, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 50, 50, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450240 none CC1C(NC(=O)C2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 40, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 121] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450240 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450240 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450240/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450240 Building REAL300024450241 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450241' /scratch/stefan/7786230/working/building/REAL300024450241 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450241 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450241/0 /scratch/stefan/7786230/working/building/REAL300024450241 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/99 `/scratch/stefan/7786230/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450241/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450241 none CC1C(NC(=O)C2=CN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 33, 49, 83, 83, 83, 83, 83, 10, 10, 10, 10, 10, 6, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10, 33, 33, 83] 83 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 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: REAL300024450241 none CC1C(NC(=O)C2=CN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 78, 78, 78, 83, 83, 83, 83, 83, 74, 74, 74, 72, 39, 72, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 78, 83, 83, 83, 83, 83, 74, 74, 74, 74, 74, 74, 39, 39, 1] 83 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 274 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450241 none CC1C(NC(=O)C2=CN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 15, 30, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 15, 15, 74] 83 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450241 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450241 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450241/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450241 Building REAL300024450242 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450242' /scratch/stefan/7786230/working/building/REAL300024450242 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450242 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450242/0 /scratch/stefan/7786230/working/building/REAL300024450242 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/100 `/scratch/stefan/7786230/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2COC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450242/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450242 none CC1C(NC(=O)CC2COC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 57, 57, 103, 139, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 27, 6, 6, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 103, 103, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 579 number of broken/clashed sets: 7 ./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: REAL300024450242 none CC1C(NC(=O)CC2COC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 92, 92, 92, 183, 201, 201, 201, 201, 201, 76, 76, 76, 72, 27, 72, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 92, 183, 183, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 27, 27, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450242 none CC1C(NC(=O)CC2COC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 19, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 10, 17, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 5, 19, 19, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 10, 10, 76] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 247 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450242 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450242 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450242/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450242 Building REAL300024450243 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450243' /scratch/stefan/7786230/working/building/REAL300024450243 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450243 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450243/0 /scratch/stefan/7786230/working/building/REAL300024450243 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/101 `/scratch/stefan/7786230/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450243/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450243 none CC1=C(C)OC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 74, 74, 74, 74, 74, 1, 1, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 74, 1, 2, 2, 2, 10] 106 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 168 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: REAL300024450243 none CC1=C(C)OC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 101, 101, 101, 74, 74, 74, 74, 74, 71, 39, 71, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 106, 106, 106, 106, 106, 106, 106, 101, 74, 74, 74, 74, 74, 74, 74, 39, 39, 1, 74, 74, 74, 74, 106] 106 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 346 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450243 none CC1=C(C)OC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 15, 15, 41, 59, 106, 106, 106, 106, 106, 10, 10, 1, 2, 2, 2, 1, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 41, 41, 106, 10, 10, 10, 10, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 276 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450243 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450243 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450243/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450243 Building REAL300024450244 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450244' /scratch/stefan/7786230/working/building/REAL300024450244 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450244 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450244/0 /scratch/stefan/7786230/working/building/REAL300024450244 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/102 `/scratch/stefan/7786230/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450244/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450244 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 36, 36, 86, 132, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 17, 7, 7, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 86, 86, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 571 number of broken/clashed sets: 54 ./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: REAL300024450244 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 33, 33, 53, 53, 53, 122, 201, 201, 201, 201, 201, 33, 33, 33, 33, 22, 33, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 53, 122, 122, 201, 201, 201, 201, 33, 33, 33, 33, 33, 33, 22, 22, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 649 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450244 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 6, 10, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 4, 12, 12, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 6, 6, 33] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450244 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450244 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450244/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450244 Building REAL300024450245 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450245' /scratch/stefan/7786230/working/building/REAL300024450245 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450245 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450245/0 /scratch/stefan/7786230/working/building/REAL300024450245 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/103 `/scratch/stefan/7786230/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450245/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450245 none CC1C(NC(=O)C2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 78, 117, 178, 178, 178, 178, 178, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 78, 78, 178] 178 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 459 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: REAL300024450245 none CC1C(NC(=O)C2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 123, 123, 123, 178, 178, 178, 178, 178, 105, 105, 105, 97, 41, 97, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 123, 178, 178, 178, 178, 178, 178, 178, 178, 178, 105, 105, 105, 105, 105, 105, 41, 41, 1] 178 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 572 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450245 none CC1C(NC(=O)C2CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 16, 33, 105, 105, 105, 105, 105, 2, 2, 2, 1, 1, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 16, 16, 105] 178 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450245 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450245 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450245/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450245 Building REAL300024450246 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450246' /scratch/stefan/7786230/working/building/REAL300024450246 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450246 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450246/0 /scratch/stefan/7786230/working/building/REAL300024450246 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/104 `/scratch/stefan/7786230/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1=O) `REAL300024450246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450246/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450246 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 87, 87, 87, 87, 87, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 87, 1, 2, 2, 2] 193 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 41 ./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: REAL300024450246 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [193, 193, 193, 193, 110, 110, 110, 87, 87, 87, 87, 87, 82, 40, 82, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 193, 193, 193, 193, 193, 193, 193, 110, 87, 87, 87, 87, 87, 87, 87, 40, 40, 1, 87, 87, 87, 87] 193 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 615 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450246 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 13, 13, 13, 29, 29, 29, 29, 29, 41, 41, 94, 128, 193, 193, 193, 193, 193, 29, 29, 1, 1, 2, 2, 2, 1, 1, 13, 29, 29, 29, 29, 29, 29, 29, 94, 94, 193, 29, 29, 29, 29] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 545 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450246 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450246 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450246/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450246 Building REAL300024450247 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450247' /scratch/stefan/7786230/working/building/REAL300024450247 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450247 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450247/0 /scratch/stefan/7786230/working/building/REAL300024450247 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/105 `/scratch/stefan/7786230/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(SC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450247/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450247 none CCC(SC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 6, 8, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6] 11 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 29 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450247 none CCC(SC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 5, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 1, 2, 2, 2] 11 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450247 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450247 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450247/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450247 Building REAL300024450248 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450248' /scratch/stefan/7786230/working/building/REAL300024450248 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450248 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450248/0 /scratch/stefan/7786230/working/building/REAL300024450248 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/106 `/scratch/stefan/7786230/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NC=N1) `REAL300024450248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450248/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450248 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 77, 77, 77, 77, 77, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 77, 1, 2, 2, 2, 9] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 170 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: REAL300024450248 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 105, 105, 105, 77, 77, 77, 77, 77, 73, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 107, 107, 107, 107, 107, 107, 107, 105, 77, 77, 77, 77, 77, 77, 77, 39, 39, 1, 77, 77, 77, 77, 107] 107 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46]) total number of confs: 348 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450248 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 14, 14, 42, 60, 107, 107, 107, 107, 107, 9, 9, 1, 1, 1, 2, 2, 2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 42, 42, 107, 9, 9, 9, 9, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450248 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450248 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450248/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450248 Building REAL300024450249 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450249' /scratch/stefan/7786230/working/building/REAL300024450249 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450249 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450249/0 /scratch/stefan/7786230/working/building/REAL300024450249 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/107 `/scratch/stefan/7786230/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450249/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450249 none CC1C(NC(=O)C2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 50, 102, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 50, 50, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 439 number of broken/clashed sets: 25 ./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: REAL300024450249 none CC1C(NC(=O)C2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 121, 121, 121, 135, 135, 135, 201, 201, 201, 201, 121, 121, 121, 120, 52, 120, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 52, 52, 1] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 661 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450249 none CC1C(NC(=O)C2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 12, 32, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 121] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450249 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450249 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450249/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450249 Building REAL300024450250 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450250' /scratch/stefan/7786230/working/building/REAL300024450250 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450250 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450250/0 /scratch/stefan/7786230/working/building/REAL300024450250 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/108 `/scratch/stefan/7786230/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450250/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450250 none CCC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 188, 120, 120, 120, 90, 90, 90, 90, 90, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 120, 90, 90, 90, 90, 90, 90, 90, 30, 30, 1, 90, 90, 90, 90] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 731 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450250 none CCC(C)OCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 29, 37, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 90, 90, 90, 90, 90, 1, 1, 39, 39, 39, 39, 39, 37, 37, 37, 37, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 90, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 269 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450250 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450250 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450250/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450250 Building REAL300024450251 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450251' /scratch/stefan/7786230/working/building/REAL300024450251 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450251 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450251/0 /scratch/stefan/7786230/working/building/REAL300024450251 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/109 `/scratch/stefan/7786230/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450251/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450251 none CC1C(NC(=O)[C@H]2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 49, 104, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 7, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 49, 49, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 437 number of broken/clashed sets: 23 ./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: REAL300024450251 none CC1C(NC(=O)[C@H]2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 128, 128, 128, 201, 201, 201, 201, 201, 115, 115, 115, 114, 48, 114, 12, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 128, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 115, 115, 48, 48, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 685 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450251 none CC1C(NC(=O)[C@H]2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 12, 36, 115, 115, 115, 115, 115, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 115] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450251 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450251 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450251/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450251 Building REAL300024450252 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450252' /scratch/stefan/7786230/working/building/REAL300024450252 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450252 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450252/0 /scratch/stefan/7786230/working/building/REAL300024450252 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/110 `/scratch/stefan/7786230/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450252/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450252 none CC1C(NC(=O)CC(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 18, 18, 12, 18, 4, 1, 4, 4, 1, 1, 1, 25, 25, 25, 25, 25, 39, 39, 87, 124, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 18, 12, 12, 4, 4, 4, 12, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 87, 87, 201] 603 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 580 number of broken/clashed sets: 100 ./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: REAL300024450252 none CC1C(NC(=O)CC(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 107, 107, 107, 176, 197, 201, 201, 201, 201, 91, 91, 91, 83, 28, 83, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 107, 176, 176, 201, 201, 201, 603, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 28, 28, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1418 number of broken/clashed sets: 100 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450252 none CC1C(NC(=O)CC(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 11, 18, 20, 20, 25, 25, 1, 1, 1, 1, 1, 3, 3, 12, 27, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 3, 11, 11, 20, 20, 20, 60, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 12, 12, 91] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 327 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450252 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450252 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450252/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450252 Building REAL300024450253 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450253' /scratch/stefan/7786230/working/building/REAL300024450253 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450253 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450253/0 /scratch/stefan/7786230/working/building/REAL300024450253 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/111 `/scratch/stefan/7786230/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450253/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450253 none CSC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 179, 152, 179, 72, 72, 72, 62, 62, 62, 62, 62, 60, 27, 60, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 179, 179, 179, 179, 152, 152, 72, 62, 62, 62, 62, 62, 62, 62, 27, 27, 1, 62, 62, 62, 62] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 789 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450253 none CSC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 14, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 62, 62, 62, 62, 62, 1, 1, 35, 35, 35, 20, 20, 20, 20, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 62, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450253 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450253 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450253/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450253 Building REAL300024450254 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450254' /scratch/stefan/7786230/working/building/REAL300024450254 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450254 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450254/0 /scratch/stefan/7786230/working/building/REAL300024450254 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/112 `/scratch/stefan/7786230/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450254/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450254 none CC1C(NC(=O)CN2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 35, 35, 82, 125, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 82, 82, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 525 number of broken/clashed sets: 18 ./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: REAL300024450254 none CC1C(NC(=O)CN2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 85, 85, 85, 99, 99, 99, 199, 201, 201, 201, 201, 201, 85, 85, 85, 77, 28, 77, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 99, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 85, 85, 85, 28, 28, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 741 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450254 none CC1C(NC(=O)CN2CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 12, 23, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 3, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 12, 12, 85] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450254 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450254 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450254/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450254 Building REAL300024450255 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450255' /scratch/stefan/7786230/working/building/REAL300024450255 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450255 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450255/0 /scratch/stefan/7786230/working/building/REAL300024450255 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/113 `/scratch/stefan/7786230/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450255/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450255 none CC1C(NC(=O)[C@@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 71, 125, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 71, 71, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 486 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: REAL300024450255 none CC1C(NC(=O)[C@@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [119, 119, 119, 119, 127, 127, 127, 201, 201, 201, 201, 201, 119, 119, 119, 116, 52, 116, 12, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 127, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 52, 52, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 631 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450255 none CC1C(NC(=O)[C@@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 14, 38, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 14, 14, 119] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 227 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450255 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450255 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450255/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450255 Building REAL300024450256 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450256' /scratch/stefan/7786230/working/building/REAL300024450256 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450256 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450256/0 /scratch/stefan/7786230/working/building/REAL300024450256 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/114 `/scratch/stefan/7786230/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NC=N1) `REAL300024450256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450256/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450256 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 85, 85, 85, 77, 77, 77, 77, 77, 71, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 190, 201, 201, 201, 201, 190, 190, 190, 190, 85, 77, 77, 77, 77, 77, 77, 77, 28, 28, 1, 77, 77, 77, 77, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 721 number of broken/clashed sets: 7 ./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: REAL300024450256 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 29, 29, 29, 33, 33, 33, 33, 33, 42, 42, 86, 127, 201, 201, 201, 201, 201, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 33, 33, 33, 33, 33, 33, 33, 86, 86, 201, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [1, 46, 47, 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]) total number of confs: 525 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450256 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 77, 77, 77, 77, 77, 1, 1, 14, 33, 33, 33, 33, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 77, 1, 2, 2, 2, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450256 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450256 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450256/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450256 Building REAL300024450257 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450257' /scratch/stefan/7786230/working/building/REAL300024450257 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450257 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450257/0 /scratch/stefan/7786230/working/building/REAL300024450257 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/115 `/scratch/stefan/7786230/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2COCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450257/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450257 none CC1C(NC(=O)C2COCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 35, 59, 102, 102, 102, 102, 102, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 35, 35, 102] 102 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 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: REAL300024450257 none CC1C(NC(=O)C2COCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 83, 83, 83, 102, 102, 102, 102, 102, 102, 80, 80, 80, 75, 36, 75, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 83, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 80, 80, 80, 80, 80, 80, 36, 36, 1] 102 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 341 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450257 none CC1C(NC(=O)C2COCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 16, 31, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 16, 16, 80] 102 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450257 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450257 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450257/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450257 Building REAL300024450258 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450258' /scratch/stefan/7786230/working/building/REAL300024450258 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450258 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450258/0 /scratch/stefan/7786230/working/building/REAL300024450258 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/116 `/scratch/stefan/7786230/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450258/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450258 none CC1=NSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 14, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 28, 81, 81, 81, 81, 81, 1, 1, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 81, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 18 ./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: REAL300024450258 none CC1=NSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 106, 106, 106, 81, 81, 81, 81, 81, 78, 45, 78, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 106, 81, 81, 81, 81, 81, 81, 81, 45, 45, 1, 81, 81, 81, 81] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 518 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450258 none CC1=NSC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 16, 16, 16, 16, 16, 24, 24, 60, 100, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 9, 16, 16, 16, 16, 16, 16, 16, 60, 60, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 472 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450258 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450258 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450258/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450258 Building REAL300024450259 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450259' /scratch/stefan/7786230/working/building/REAL300024450259 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450259 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450259/0 /scratch/stefan/7786230/working/building/REAL300024450259 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/117 `/scratch/stefan/7786230/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450259/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450259 none C#CCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 167, 157, 146, 46, 46, 46, 37, 37, 37, 37, 37, 36, 20, 36, 12, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 167, 167, 167, 167, 146, 146, 46, 37, 37, 37, 37, 37, 37, 37, 20, 20, 1, 37, 37, 37, 37] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 917 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450259 none C#CCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 22, 20, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 37, 37, 37, 37, 37, 1, 1, 53, 53, 53, 22, 22, 22, 22, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 318 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450259 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450259 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450259/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450259 Building REAL300024450260 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450260' /scratch/stefan/7786230/working/building/REAL300024450260 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450260 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450260/0 /scratch/stefan/7786230/working/building/REAL300024450260 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/118 `/scratch/stefan/7786230/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450260/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450260 none C#CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 167, 201, 64, 64, 64, 48, 48, 48, 48, 48, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 167, 167, 64, 48, 48, 48, 48, 48, 48, 48, 26, 26, 1, 48, 48, 48, 48] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 789 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450260 none C#CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 26, 26, 15, 26, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 48, 48, 48, 48, 48, 1, 1, 43, 43, 43, 26, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 48, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450260 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450260 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450260/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450260 Building REAL300024450261 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450261' /scratch/stefan/7786230/working/building/REAL300024450261 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450261 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450261/0 /scratch/stefan/7786230/working/building/REAL300024450261 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/119 `/scratch/stefan/7786230/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450261/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450261 none CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 158, 159, 73, 73, 73, 51, 51, 51, 51, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 159, 158, 158, 73, 51, 51, 51, 51, 51, 51, 51, 28, 28, 1, 51, 51, 51, 51] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 895 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450261 none CCNC(=O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 24, 24, 15, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 51, 51, 51, 51, 51, 1, 1, 44, 44, 44, 44, 44, 24, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 51, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450261 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450261 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450261/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450261 Building REAL300024450262 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450262' /scratch/stefan/7786230/working/building/REAL300024450262 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450262 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450262/0 /scratch/stefan/7786230/working/building/REAL300024450262 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/120 `/scratch/stefan/7786230/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450262/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450262 none CNC(=O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 201, 153, 163, 60, 60, 60, 54, 54, 54, 54, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 188, 187, 183, 183, 163, 163, 60, 54, 54, 54, 54, 54, 54, 54, 29, 29, 1, 54, 54, 54, 54] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 958 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450262 none CNC(=O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 33, 47, 18, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 54, 54, 54, 54, 54, 1, 1, 47, 47, 47, 47, 30, 30, 22, 22, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450262 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450262 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450262/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450262 Building REAL300024450263 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450263' /scratch/stefan/7786230/working/building/REAL300024450263 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450263 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450263/0 /scratch/stefan/7786230/working/building/REAL300024450263 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/121 `/scratch/stefan/7786230/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450263/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450263 none COC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 63, 63, 63, 63, 63, 1, 1, 9, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 1, 2, 2, 2, 9] 86 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 18 ./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: REAL300024450263 none COC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 69, 69, 69, 63, 63, 63, 63, 63, 62, 38, 62, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 86, 86, 86, 86, 69, 63, 63, 63, 63, 63, 63, 63, 38, 38, 1, 63, 63, 63, 63, 86] 86 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450263 none COC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 13, 13, 32, 48, 86, 86, 86, 86, 86, 9, 9, 1, 3, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 32, 32, 86, 9, 9, 9, 9, 1] 86 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450263 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450263 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450263/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450263 Building REAL300024450264 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450264' /scratch/stefan/7786230/working/building/REAL300024450264 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450264 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450264/0 /scratch/stefan/7786230/working/building/REAL300024450264 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/122 `/scratch/stefan/7786230/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450264/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450264 none COC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 201, 180, 81, 81, 81, 63, 63, 63, 63, 63, 62, 25, 62, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 195, 195, 180, 180, 81, 63, 63, 63, 63, 63, 63, 63, 25, 25, 1, 63, 63, 63, 63] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 809 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450264 none COC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 22, 30, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 63, 63, 63, 63, 63, 1, 1, 30, 30, 30, 30, 30, 30, 30, 23, 23, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450264 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450264 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450264/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450264 Building REAL300024450265 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450265' /scratch/stefan/7786230/working/building/REAL300024450265 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450265 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450265/0 /scratch/stefan/7786230/working/building/REAL300024450265 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/123 `/scratch/stefan/7786230/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1) `REAL300024450265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450265/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450265 none CCC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 8, 8, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 29, 110, 110, 110, 110, 110, 1, 1, 8, 8, 30, 30, 30, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 110, 1, 2, 2, 2, 8] 185 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 286 number of broken/clashed sets: 33 ./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: REAL300024450265 none CCC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [185, 150, 150, 150, 147, 147, 147, 110, 110, 110, 110, 110, 102, 43, 102, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 150, 150, 185, 185, 185, 185, 185, 147, 110, 110, 110, 110, 110, 110, 110, 43, 43, 1, 110, 110, 110, 110, 150] 185 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450265 none CCC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 12, 12, 39, 62, 150, 150, 150, 150, 150, 8, 8, 1, 1, 9, 9, 9, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 39, 39, 150, 8, 8, 8, 8, 1] 185 rigid atoms, others: [1, 2, 3, 4, 5, 47, 25, 26] set([0, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 343 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450265 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450265 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450265/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450265 Building REAL300024450266 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450266' /scratch/stefan/7786230/working/building/REAL300024450266 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450266 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450266/0 /scratch/stefan/7786230/working/building/REAL300024450266 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/124 `/scratch/stefan/7786230/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450266/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450266 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 28, 45, 86, 86, 86, 86, 86, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 86] 86 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 18 ./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: REAL300024450266 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 86, 86, 86, 86, 86, 86, 86, 86, 86, 82, 82, 82, 79, 41, 79, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 86, 86, 86, 86, 82, 82, 82, 82, 82, 82, 41, 41, 1] 86 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 288 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450266 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 3, 3, 15, 32, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 15, 82] 86 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450266 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450266 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450266/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450266 Building REAL300024450267 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450267' /scratch/stefan/7786230/working/building/REAL300024450267 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450267 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450267/0 /scratch/stefan/7786230/working/building/REAL300024450267 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/125 `/scratch/stefan/7786230/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(N)N(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450267/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450267 none CC1C(NC(=O)C2=C(N)N(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 55, 88, 150, 150, 150, 150, 150, 12, 12, 12, 12, 12, 9, 2, 2, 2, 2, 2, 1, 12, 12, 12, 12, 12, 12, 55, 55, 150] 150 rigid atoms, others: [4, 38, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 371 number of broken/clashed sets: 95 ./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: REAL300024450267 none CC1C(NC(=O)C2=C(N)N(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 90, 90, 90, 150, 150, 150, 150, 150, 150, 80, 80, 80, 78, 40, 78, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 90, 150, 150, 150, 150, 150, 150, 80, 80, 80, 80, 80, 80, 40, 40, 1] 150 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 402 number of broken/clashed sets: 95 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450267 none CC1C(NC(=O)C2=C(N)N(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 27, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 80] 150 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450267 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450267 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450267/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450267 Building REAL300024450268 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450268' /scratch/stefan/7786230/working/building/REAL300024450268 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450268 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450268/0 /scratch/stefan/7786230/working/building/REAL300024450268 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/126 `/scratch/stefan/7786230/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450268/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450268 none CC1C(NC(=O)C2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 44, 102, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 44, 44, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 402 number of broken/clashed sets: 31 ./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: REAL300024450268 none CC1C(NC(=O)C2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 168, 68, 168, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 68, 68, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 627 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450268 none CC1C(NC(=O)C2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 6, 6, 4, 6, 6, 1, 1, 1, 1, 1, 4, 4, 16, 56, 175, 175, 175, 175, 175, 2, 2, 2, 1, 1, 4, 6, 4, 6, 1, 1, 1, 1, 1, 1, 16, 16, 175] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 293 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450268 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450268 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450268/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450268 Building REAL300024450269 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450269' /scratch/stefan/7786230/working/building/REAL300024450269 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450269 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450269/0 /scratch/stefan/7786230/working/building/REAL300024450269 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/127 `/scratch/stefan/7786230/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450269/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450269 none CC1C(NC(=O)C2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 26, 26, 73, 129, 201, 201, 201, 201, 201, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 73, 73, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 496 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: REAL300024450269 none CC1C(NC(=O)C2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [149, 149, 149, 149, 180, 180, 180, 201, 201, 201, 201, 201, 149, 149, 149, 144, 56, 144, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 180, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 149, 56, 56, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 609 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450269 none CC1C(NC(=O)C2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 11, 32, 149, 149, 149, 149, 149, 2, 2, 2, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 11, 11, 149] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450269 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450269 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450269/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450269 Building REAL300024450270 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450270' /scratch/stefan/7786230/working/building/REAL300024450270 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450270 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450270/0 /scratch/stefan/7786230/working/building/REAL300024450270 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/128 `/scratch/stefan/7786230/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450270/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450270 none CC1C(NC(=O)CC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 15, 15, 4, 15, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 37, 37, 86, 127, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 15, 4, 4, 1, 1, 1, 29, 29, 29, 29, 29, 29, 86, 86, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 44 ./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: REAL300024450270 none CC1C(NC(=O)CC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 37, 44, 44, 44, 92, 201, 201, 201, 201, 37, 37, 37, 35, 26, 35, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 44, 92, 92, 201, 201, 201, 37, 37, 37, 37, 37, 37, 26, 26, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450270 none CC1C(NC(=O)CC2=COC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 7, 11, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 4, 11, 11, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 7, 37] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450270 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450270 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450270/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450270 Building REAL300024450271 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450271' /scratch/stefan/7786230/working/building/REAL300024450271 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450271 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450271/0 /scratch/stefan/7786230/working/building/REAL300024450271 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/129 `/scratch/stefan/7786230/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1) `REAL300024450271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450271/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450271 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 70, 70, 70, 70, 70, 1, 1, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 70, 1, 2, 2, 2, 8] 75 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 158 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: REAL300024450271 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 73, 73, 73, 70, 70, 70, 70, 70, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 75, 75, 75, 75, 75, 73, 70, 70, 70, 70, 70, 70, 70, 38, 38, 1, 70, 70, 70, 70, 75] 75 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450271 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 5, 8, 8, 8, 8, 8, 10, 10, 28, 43, 75, 75, 75, 75, 75, 8, 8, 1, 1, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 8, 28, 28, 75, 8, 8, 8, 8, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450271 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450271 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450271/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450271 Building REAL300024450272 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450272' /scratch/stefan/7786230/working/building/REAL300024450272 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450272 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450272/0 /scratch/stefan/7786230/working/building/REAL300024450272 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/130 `/scratch/stefan/7786230/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450272/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450272 none CC1C(NC(=O)C2=CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 24, 24, 74, 116, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 74, 74, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 494 number of broken/clashed sets: 46 ./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: REAL300024450272 none CC1C(NC(=O)C2=CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 78, 78, 78, 201, 201, 201, 201, 201, 201, 76, 76, 76, 73, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 39, 39, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 427 number of broken/clashed sets: 46 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450272 none CC1C(NC(=O)C2=CCCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 12, 24, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 12, 12, 76] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450272 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450272 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450272/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450272 Building REAL300024450273 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450273' /scratch/stefan/7786230/working/building/REAL300024450273 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450273 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450273/0 /scratch/stefan/7786230/working/building/REAL300024450273 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/131 `/scratch/stefan/7786230/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450273/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450273 none C[C@H](NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [163, 127, 163, 163, 163, 163, 163, 127, 127, 112, 112, 112, 112, 112, 106, 31, 106, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 163, 163, 163, 163, 163, 163, 127, 112, 112, 112, 112, 112, 112, 112, 31, 31, 1, 112, 112, 112, 112] 163 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 566 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450273 none C[C@H](NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 4, 13, 13, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 30, 112, 112, 112, 112, 112, 1, 1, 13, 13, 13, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 112, 1, 2, 2, 2] 163 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450273 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450273 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450273/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450273 Building REAL300024450274 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450274' /scratch/stefan/7786230/working/building/REAL300024450274 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450274 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450274/0 /scratch/stefan/7786230/working/building/REAL300024450274 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/132 `/scratch/stefan/7786230/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2OCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450274/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450274 none CC1C(NC(=O)CC2OCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 23, 23, 6, 23, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 44, 44, 83, 129, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 83, 83, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 547 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: REAL300024450274 none CC1C(NC(=O)CC2OCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 98, 98, 98, 184, 201, 201, 201, 201, 201, 80, 80, 80, 77, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 98, 184, 184, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 80, 30, 30, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 740 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450274 none CC1C(NC(=O)CC2OCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 12, 22, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 3, 16, 16, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 12, 12, 80] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450274 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450274 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450274/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450274 Building REAL300024450275 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450275' /scratch/stefan/7786230/working/building/REAL300024450275 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450275 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450275/0 /scratch/stefan/7786230/working/building/REAL300024450275 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/133 `/scratch/stefan/7786230/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1) `REAL300024450275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450275/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450275 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 42, 138, 138, 138, 138, 138, 1, 1, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 138, 1, 2, 2, 2, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 233 number of broken/clashed sets: 25 ./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: REAL300024450275 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 153, 153, 153, 138, 138, 138, 138, 138, 135, 58, 135, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 153, 138, 138, 138, 138, 138, 138, 138, 58, 58, 1, 138, 138, 138, 138, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45]) total number of confs: 571 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450275 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 9, 9, 9, 9, 9, 15, 15, 52, 108, 201, 201, 201, 201, 201, 9, 9, 1, 1, 2, 2, 2, 1, 5, 9, 9, 9, 9, 9, 9, 9, 52, 52, 201, 9, 9, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 446 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450275 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450275 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450275/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450275 Building REAL300024450276 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450276' /scratch/stefan/7786230/working/building/REAL300024450276 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450276 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450276/0 /scratch/stefan/7786230/working/building/REAL300024450276 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/134 `/scratch/stefan/7786230/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=C1) `REAL300024450276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450276/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450276 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 32, 103, 103, 103, 103, 103, 1, 1, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 103, 1, 2, 2, 2, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 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: REAL300024450276 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 113, 113, 113, 103, 103, 103, 103, 103, 101, 48, 101, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 113, 103, 103, 103, 103, 103, 103, 103, 48, 48, 1, 103, 103, 103, 103, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 491 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450276 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 12, 12, 12, 12, 12, 19, 19, 56, 107, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 1, 2, 2, 2, 9, 12, 12, 12, 12, 12, 12, 12, 56, 56, 201, 12, 12, 12, 12, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 462 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450276 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450276 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450276/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450276 Building REAL300024450277 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450277' /scratch/stefan/7786230/working/building/REAL300024450277 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450277 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450277/0 /scratch/stefan/7786230/working/building/REAL300024450277 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/135 `/scratch/stefan/7786230/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1) `REAL300024450277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450277/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450277 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 38, 109, 109, 109, 109, 109, 1, 1, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 109, 1, 2, 2, 2, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 31 ./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: REAL300024450277 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 115, 115, 109, 109, 109, 109, 109, 107, 54, 107, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 115, 109, 109, 109, 109, 109, 109, 109, 54, 54, 1, 109, 109, 109, 109, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46]) total number of confs: 497 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450277 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 8, 8, 8, 8, 8, 14, 14, 47, 97, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 2, 2, 2, 1, 5, 8, 8, 8, 8, 8, 8, 8, 47, 47, 201, 8, 8, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 430 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450277 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450277 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450277/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450277 Building REAL300024450278 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450278' /scratch/stefan/7786230/working/building/REAL300024450278 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450278 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450278/0 /scratch/stefan/7786230/working/building/REAL300024450278 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/136 `/scratch/stefan/7786230/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450278/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450278 none CC1C(NC(=O)CCN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 42, 35, 35, 11, 35, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 50, 50, 98, 139, 201, 201, 201, 201, 201, 42, 42, 42, 42, 42, 35, 11, 11, 6, 6, 1, 1, 42, 42, 42, 42, 42, 42, 98, 98, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 586 number of broken/clashed sets: 35 ./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: REAL300024450278 none CC1C(NC(=O)CCN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 74, 74, 74, 170, 184, 201, 201, 201, 201, 58, 58, 58, 56, 35, 56, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 74, 170, 170, 184, 184, 201, 201, 58, 58, 58, 58, 58, 58, 35, 35, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 773 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450278 none CC1C(NC(=O)CCN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 21, 42, 42, 42, 42, 1, 1, 1, 1, 1, 3, 3, 10, 17, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 15, 15, 21, 21, 42, 42, 1, 1, 1, 1, 1, 1, 10, 10, 58] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450278 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450278 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450278/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450278 Building REAL300024450279 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450279' /scratch/stefan/7786230/working/building/REAL300024450279 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450279 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450279/0 /scratch/stefan/7786230/working/building/REAL300024450279 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/137 `/scratch/stefan/7786230/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450279/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450279 none CC(=O)N1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 18, 29, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 46, 46, 46, 46, 46, 1, 1, 18, 29, 29, 29, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 1, 2, 2, 2, 18, 18] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 40 ./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: REAL300024450279 none CC(=O)N1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 136, 201, 136, 136, 56, 56, 56, 46, 46, 46, 46, 46, 44, 31, 44, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 136, 201, 201, 201, 136, 136, 136, 56, 46, 46, 46, 46, 46, 46, 46, 31, 31, 1, 46, 46, 46, 46, 136, 136] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 678 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450279 none CC(=O)N1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 18, 18, 18, 18, 18, 23, 23, 54, 82, 136, 136, 136, 136, 136, 18, 18, 1, 3, 3, 3, 1, 1, 1, 10, 18, 18, 18, 18, 18, 18, 18, 54, 54, 136, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 48, 49, 26, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 360 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450279 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450279 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450279/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450279 Building REAL300024450280 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450280' /scratch/stefan/7786230/working/building/REAL300024450280 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450280 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450280/0 /scratch/stefan/7786230/working/building/REAL300024450280 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/138 `/scratch/stefan/7786230/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)N(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450280/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450280 none CC1C(NC(=O)C2=CC(=O)N(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 19, 19, 52, 73, 120, 120, 120, 120, 120, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 52, 52, 120] 120 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 307 number of broken/clashed sets: 24 ./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: REAL300024450280 none CC1C(NC(=O)C2=CC(=O)N(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 88, 88, 88, 120, 120, 120, 120, 120, 120, 75, 75, 75, 69, 40, 69, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 88, 120, 120, 120, 120, 75, 75, 75, 75, 75, 75, 40, 40, 1] 120 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 342 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450280 none CC1C(NC(=O)C2=CC(=O)N(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 13, 28, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 4, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 13, 13, 75] 120 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450280 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450280 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450280/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450280 Building REAL300024450281 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450281' /scratch/stefan/7786230/working/building/REAL300024450281 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450281 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450281/0 /scratch/stefan/7786230/working/building/REAL300024450281 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/139 `/scratch/stefan/7786230/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450281/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450281 none CCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 201, 68, 68, 68, 53, 53, 53, 53, 53, 52, 25, 52, 12, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 68, 53, 53, 53, 53, 53, 53, 53, 25, 25, 1, 53, 53, 53, 53] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 791 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450281 none CCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 14, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 53, 53, 53, 53, 53, 1, 1, 30, 30, 30, 30, 30, 24, 24, 24, 24, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 53, 1, 2, 2, 2] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450281 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450281 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450281/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450281 Building REAL300024450282 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450282' /scratch/stefan/7786230/working/building/REAL300024450282 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450282 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450282/0 /scratch/stefan/7786230/working/building/REAL300024450282 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/140 `/scratch/stefan/7786230/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450282/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450282 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 25, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 66, 66, 66, 66, 66, 1, 1, 25, 25, 25, 27, 27, 27, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 66, 1, 2, 2, 2, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 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: REAL300024450282 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 182, 83, 83, 83, 66, 66, 66, 66, 66, 64, 26, 64, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 182, 182, 83, 66, 66, 66, 66, 66, 66, 66, 26, 26, 1, 66, 66, 66, 66, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 773 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450282 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 18, 18, 18, 25, 25, 25, 25, 25, 44, 44, 80, 122, 201, 201, 201, 201, 201, 25, 25, 1, 1, 1, 4, 4, 4, 7, 7, 18, 25, 25, 25, 25, 25, 25, 25, 80, 80, 201, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 528 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450282 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450282 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450282/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450282 Building REAL300024450283 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450283' /scratch/stefan/7786230/working/building/REAL300024450283 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450283 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450283/0 /scratch/stefan/7786230/working/building/REAL300024450283 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/141 `/scratch/stefan/7786230/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450283/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450283 none CC1OCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 25, 68, 68, 68, 68, 68, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 68, 1, 2, 2, 2] 88 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 36 ./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: REAL300024450283 none CC1OCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 70, 70, 70, 68, 68, 68, 68, 68, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 70, 68, 68, 68, 68, 68, 68, 68, 38, 38, 1, 68, 68, 68, 68] 88 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 299 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450283 none CC1OCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 12, 12, 33, 50, 88, 88, 88, 88, 88, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 33, 33, 88, 7, 7, 7, 7] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450283 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450283 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450283/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450283 Building REAL300024450284 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450284' /scratch/stefan/7786230/working/building/REAL300024450284 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450284 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450284/0 /scratch/stefan/7786230/working/building/REAL300024450284 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/142 `/scratch/stefan/7786230/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450284/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450284 none C#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 153, 48, 48, 48, 40, 40, 40, 40, 40, 39, 23, 39, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 201, 189, 187, 172, 172, 153, 153, 48, 40, 40, 40, 40, 40, 40, 40, 23, 23, 1, 40, 40, 40, 40] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 952 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450284 none C#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 19, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 40, 40, 40, 40, 40, 1, 1, 46, 42, 43, 24, 24, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 294 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450284 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450284 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450284/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450284 Building REAL300024450285 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450285' /scratch/stefan/7786230/working/building/REAL300024450285 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450285 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450285/0 /scratch/stefan/7786230/working/building/REAL300024450285 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/143 `/scratch/stefan/7786230/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(Cl)OC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450285/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450285 none CC1C(NC(=O)C2=C(Cl)OC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 44, 87, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 9, 9, 9, 9, 9, 9, 44, 44, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 422 number of broken/clashed sets: 22 ./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: REAL300024450285 none CC1C(NC(=O)C2=C(Cl)OC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 66, 66, 66, 201, 201, 201, 201, 201, 66, 66, 66, 64, 35, 64, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 201, 201, 66, 66, 66, 66, 66, 66, 35, 35, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450285 none CC1C(NC(=O)C2=C(Cl)OC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 11, 23, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 3, 9, 9, 1, 1, 1, 1, 1, 1, 11, 11, 66] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450285 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450285 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450285/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450285 Building REAL300024450286 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450286' /scratch/stefan/7786230/working/building/REAL300024450286 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450286 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450286/0 /scratch/stefan/7786230/working/building/REAL300024450286 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/144 `/scratch/stefan/7786230/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NS1) `REAL300024450286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450286/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450286 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 28, 61, 61, 61, 61, 61, 1, 1, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 61, 1, 2, 2, 2] 84 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 145 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: REAL300024450286 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 78, 78, 78, 61, 61, 61, 61, 61, 58, 34, 58, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 84, 84, 84, 84, 84, 84, 78, 61, 61, 61, 61, 61, 61, 61, 34, 34, 1, 61, 61, 61, 61] 84 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44]) total number of confs: 274 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450286 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 11, 11, 36, 52, 84, 84, 84, 84, 84, 9, 9, 1, 1, 2, 2, 2, 1, 5, 9, 9, 9, 9, 9, 9, 9, 36, 36, 84, 9, 9, 9, 9] 84 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450286 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450286 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450286/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450286 Building REAL300024450287 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450287' /scratch/stefan/7786230/working/building/REAL300024450287 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450287 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450287/0 /scratch/stefan/7786230/working/building/REAL300024450287 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/145 `/scratch/stefan/7786230/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450287/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450287 none CCN1C=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 83, 83, 83, 83, 83, 1, 1, 18, 18, 18, 18, 18, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 83, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 10 ./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: REAL300024450287 none CCN1C=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 121, 121, 121, 121, 121, 110, 110, 110, 83, 83, 83, 83, 83, 79, 29, 79, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 121, 121, 110, 83, 83, 83, 83, 83, 83, 83, 29, 29, 1, 83, 83, 83, 83] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 846 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450287 none CCN1C=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 13, 13, 40, 66, 121, 121, 121, 121, 121, 9, 9, 5, 5, 5, 5, 5, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 40, 40, 121, 9, 9, 9, 9] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 303 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450287 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450287 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450287/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450287 Building REAL300024450288 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450288' /scratch/stefan/7786230/working/building/REAL300024450288 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450288 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450288/0 /scratch/stefan/7786230/working/building/REAL300024450288 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/146 `/scratch/stefan/7786230/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450288/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450288 none CC1C(NC(=O)C2CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 29, 29, 76, 105, 171, 171, 171, 171, 171, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 76, 76, 171] 171 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 462 number of broken/clashed sets: 31 ./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: REAL300024450288 none CC1C(NC(=O)C2CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [78, 78, 78, 78, 109, 109, 109, 171, 171, 171, 171, 171, 171, 78, 78, 78, 71, 39, 71, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 109, 171, 171, 171, 171, 171, 171, 171, 171, 171, 171, 171, 78, 78, 78, 78, 78, 78, 39, 39, 1] 171 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 566 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450288 none CC1C(NC(=O)C2CCCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 16, 28, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 16, 16, 78] 171 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450288 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450288 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450288/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450288 Building REAL300024450289 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450289' /scratch/stefan/7786230/working/building/REAL300024450289 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450289 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450289/0 /scratch/stefan/7786230/working/building/REAL300024450289 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/147 `/scratch/stefan/7786230/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450289/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450289 none CC1C(NC(=O)CCC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 35, 35, 13, 35, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 45, 45, 79, 101, 150, 150, 150, 150, 150, 37, 37, 37, 37, 37, 35, 13, 13, 8, 8, 1, 1, 1, 37, 37, 37, 37, 37, 37, 79, 79, 150] 150 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 440 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: REAL300024450289 none CC1C(NC(=O)CCC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 23, 23, 23, 46, 46, 46, 46, 46, 46, 22, 22, 22, 22, 18, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 23, 46, 46, 46, 46, 46, 46, 46, 22, 22, 22, 22, 22, 22, 18, 18, 1] 46 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 165 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450289 none CC1C(NC(=O)CCC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 10, 14, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 7, 11, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 3, 10, 10, 14, 14, 18, 18, 18, 1, 1, 1, 1, 1, 1, 7, 7, 22] 46 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450289 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450289 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450289/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450289 Building REAL300024450290 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450290' /scratch/stefan/7786230/working/building/REAL300024450290 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450290 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450290/0 /scratch/stefan/7786230/working/building/REAL300024450290 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/148 `/scratch/stefan/7786230/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450290/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450290 none CC1C(NC(=O)C2CCC(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 549 conformations in input total number of sets (complete confs): 549 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 34, 34, 85, 119, 183, 183, 183, 183, 183, 24, 24, 24, 24, 24, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 85, 85, 183] 549 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 510 number of broken/clashed sets: 96 ./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: REAL300024450290 none CC1C(NC(=O)C2CCC(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 549 conformations in input total number of sets (complete confs): 549 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 102, 102, 102, 183, 183, 183, 183, 183, 183, 81, 81, 81, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 102, 183, 183, 183, 183, 183, 183, 549, 183, 183, 183, 183, 81, 81, 81, 81, 81, 81, 40, 40, 1] 549 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1118 number of broken/clashed sets: 96 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450290 none CC1C(NC(=O)C2CCC(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 549 conformations in input total number of sets (complete confs): 549 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 16, 28, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 6, 24, 24, 24, 24, 24, 24, 72, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 16, 16, 81] 549 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450290 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450290 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450290/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450290 Building REAL300024450291 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450291' /scratch/stefan/7786230/working/building/REAL300024450291 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450291 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450291/0 /scratch/stefan/7786230/working/building/REAL300024450291 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/149 `/scratch/stefan/7786230/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450291/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450291 none CC1C(NC(=O)CC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 118, 118, 118, 184, 199, 201, 201, 66, 66, 66, 64, 46, 64, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 118, 184, 184, 201, 201, 201, 201, 201, 201, 603, 66, 66, 66, 66, 66, 66, 46, 46, 1] 603 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 1386 number of broken/clashed sets: 176 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450291 none CC1C(NC(=O)CC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 25, 30, 30, 31, 1, 1, 1, 1, 1, 3, 3, 11, 21, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 6, 25, 25, 31, 31, 31, 31, 31, 31, 93, 1, 1, 1, 1, 1, 1, 11, 11, 66] 603 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 344 number of broken/clashed sets: 176 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450291 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450291 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450291/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450291 Building REAL300024450292 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450292' /scratch/stefan/7786230/working/building/REAL300024450292 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450292 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450292/0 /scratch/stefan/7786230/working/building/REAL300024450292 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/150 `/scratch/stefan/7786230/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450292/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450292 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 9, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 28, 69, 69, 69, 69, 69, 1, 1, 16, 16, 16, 16, 9, 16, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 69, 1, 2, 2, 2] 172 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 34 ./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: REAL300024450292 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 172, 168, 172, 172, 93, 93, 93, 69, 69, 69, 69, 69, 64, 38, 64, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 172, 172, 172, 172, 168, 172, 93, 69, 69, 69, 69, 69, 69, 69, 38, 38, 1, 69, 69, 69, 69] 172 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 475 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450292 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 24, 24, 69, 99, 172, 172, 172, 172, 172, 16, 16, 1, 2, 2, 2, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 69, 69, 172, 16, 16, 16, 16] 172 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 447 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450292 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450292 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450292/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450292 Building REAL300024450293 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450293' /scratch/stefan/7786230/working/building/REAL300024450293 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450293 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450293/0 /scratch/stefan/7786230/working/building/REAL300024450293 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/151 `/scratch/stefan/7786230/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450293/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450293 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [121, 121, 82, 82, 82, 47, 47, 47, 47, 47, 45, 39, 45, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 121, 156, 156, 121, 121, 121, 121, 82, 47, 47, 47, 47, 47, 47, 47, 39, 39, 1, 47, 47, 47, 47, 156, 156, 156, 156, 156] 156 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 595 number of broken/clashed sets: 76 ./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: REAL300024450293 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 1, 6, 19, 19, 19, 38, 38, 38, 38, 38, 50, 50, 81, 114, 156, 156, 156, 156, 156, 38, 38, 1, 1, 1, 9, 9, 9, 6, 19, 38, 38, 38, 38, 38, 38, 38, 81, 81, 156, 38, 38, 38, 38, 1, 1, 1, 1, 1] 156 rigid atoms, others: [2, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 472 number of broken/clashed sets: 76 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450293 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 47, 47, 47, 47, 47, 1, 1, 26, 38, 38, 30, 30, 30, 26, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 1, 2, 2, 2, 38, 38, 38, 38, 38] 156 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450293 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450293 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450293/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450293 Building REAL300024450294 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450294' /scratch/stefan/7786230/working/building/REAL300024450294 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450294 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450294/0 /scratch/stefan/7786230/working/building/REAL300024450294 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/152 `/scratch/stefan/7786230/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1) `REAL300024450294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450294/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450294 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 27, 108, 108, 108, 108, 108, 1, 1, 17, 17, 17, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 108, 1, 2, 2, 2, 17, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 267 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: REAL300024450294 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 195, 195, 136, 136, 136, 108, 108, 108, 108, 108, 100, 30, 100, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 195, 195, 195, 201, 201, 201, 201, 201, 136, 108, 108, 108, 108, 108, 108, 108, 30, 30, 1, 108, 108, 108, 108, 195, 195] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 543 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450294 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 17, 17, 17, 17, 17, 24, 24, 59, 99, 195, 195, 195, 195, 195, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 9, 17, 17, 17, 17, 17, 17, 17, 59, 59, 195, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 441 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450294 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450294 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450294/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450294 Building REAL300024450295 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450295' /scratch/stefan/7786230/working/building/REAL300024450295 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450295 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450295/0 /scratch/stefan/7786230/working/building/REAL300024450295 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/153 `/scratch/stefan/7786230/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450295/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450295 none CC1C(NC(=O)C2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 57, 116, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 57, 57, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 28 ./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: REAL300024450295 none CC1C(NC(=O)C2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [146, 146, 146, 146, 175, 175, 175, 201, 201, 201, 201, 201, 146, 146, 146, 142, 62, 142, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 175, 201, 201, 201, 201, 146, 146, 146, 146, 146, 146, 62, 62, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 605 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450295 none CC1C(NC(=O)C2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 14, 46, 146, 146, 146, 146, 146, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 14, 14, 146] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 251 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450295 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450295 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450295/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450295 Building REAL300024450296 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450296' /scratch/stefan/7786230/working/building/REAL300024450296 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450296 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450296/0 /scratch/stefan/7786230/working/building/REAL300024450296 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/154 `/scratch/stefan/7786230/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450296/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450296 none CCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 174, 87, 174, 87, 87, 68, 68, 68, 68, 68, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 201, 201, 200, 200, 174, 174, 174, 174, 87, 68, 68, 68, 68, 68, 68, 68, 30, 30, 1, 68, 68, 68, 68] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 823 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450296 none CCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 28, 27, 14, 4, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 68, 68, 68, 68, 68, 1, 1, 30, 30, 30, 30, 30, 28, 28, 27, 27, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 68, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450296 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450296 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450296/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450296 Building REAL300024450297 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450297' /scratch/stefan/7786230/working/building/REAL300024450297 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450297 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450297/0 /scratch/stefan/7786230/working/building/REAL300024450297 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/155 `/scratch/stefan/7786230/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450297/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450297 none CC1CC(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 72, 72, 72, 72, 72, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 72, 1, 2, 2, 2] 89 rigid atoms, others: [45, 43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 20 ./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: REAL300024450297 none CC1CC(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 86, 86, 86, 72, 72, 72, 72, 72, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 86, 72, 72, 72, 72, 72, 72, 72, 38, 38, 1, 72, 72, 72, 72] 89 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 301 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450297 none CC1CC(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 12, 12, 35, 53, 89, 89, 89, 89, 89, 8, 8, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 4, 8, 8, 8, 8, 8, 8, 8, 35, 35, 89, 8, 8, 8, 8] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 26, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 236 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450297 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450297 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450297/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450297 Building REAL300024450298 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450298' /scratch/stefan/7786230/working/building/REAL300024450298 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450298 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450298/0 /scratch/stefan/7786230/working/building/REAL300024450298 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/156 `/scratch/stefan/7786230/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450298/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450298 none CC1C(NC(=O)[C@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 50, 50, 92, 132, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 11, 1, 1, 9, 39, 39, 39, 39, 39, 39, 92, 92, 201] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 573 number of broken/clashed sets: 88 ./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: REAL300024450298 none CC1C(NC(=O)[C@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 51, 51, 51, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 48, 39, 48, 12, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 88, 201, 201, 201, 51, 51, 51, 51, 51, 51, 39, 39, 1] 201 rigid atoms, others: [45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 630 number of broken/clashed sets: 88 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450298 none CC1C(NC(=O)[C@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 39, 39, 39, 39, 39, 75, 75, 1, 1, 1, 1, 1, 3, 3, 9, 17, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 6, 39, 39, 75, 1, 1, 1, 1, 1, 1, 9, 9, 51] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 32, 40, 41, 42, 39, 14, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 361 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450298 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450298 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450298/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450298 Building REAL300024450299 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450299' /scratch/stefan/7786230/working/building/REAL300024450299 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450299 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450299/0 /scratch/stefan/7786230/working/building/REAL300024450299 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/157 `/scratch/stefan/7786230/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450299/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450299 none CC1=COC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 34, 118, 118, 118, 118, 118, 1, 1, 13, 13, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 118, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 208 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: REAL300024450299 none CC1=COC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 128, 128, 128, 118, 118, 118, 118, 118, 115, 54, 115, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 128, 118, 118, 118, 118, 118, 118, 118, 54, 54, 1, 118, 118, 118, 118] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 511 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450299 none CC1=COC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 13, 13, 13, 13, 13, 21, 21, 56, 102, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 13, 56, 56, 201, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 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, 48]) total number of confs: 459 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450299 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450299 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450299/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450299 Building REAL300024450300 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450300' /scratch/stefan/7786230/working/building/REAL300024450300 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450300 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450300/0 /scratch/stefan/7786230/working/building/REAL300024450300 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/158 `/scratch/stefan/7786230/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450300/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450300 none CC1C(NC(=O)C2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 32, 32, 87, 122, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 23, 23, 23, 23, 23, 23, 87, 87, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 41, 42] set([0, 1, 2, 3, 5, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 557 number of broken/clashed sets: 33 ./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: REAL300024450300 none CC1C(NC(=O)C2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 65, 65, 65, 80, 80, 80, 201, 201, 201, 201, 201, 65, 65, 65, 62, 39, 62, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 65, 65, 65, 39, 39, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 644 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450300 none CC1C(NC(=O)C2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 13, 21, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 13, 13, 65] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450300 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450300 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450300/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450300 Building REAL300024450301 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450301' /scratch/stefan/7786230/working/building/REAL300024450301 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450301 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450301/0 /scratch/stefan/7786230/working/building/REAL300024450301 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/159 `/scratch/stefan/7786230/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450301/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450301 none CC(C)[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 12 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 17 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450301 none CC(C)[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 12 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 34 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450301 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450301 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450301/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450301 Building REAL300024450302 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450302' /scratch/stefan/7786230/working/building/REAL300024450302 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450302 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450302/0 /scratch/stefan/7786230/working/building/REAL300024450302 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/160 `/scratch/stefan/7786230/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450302/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450302 none CCOC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 85, 85, 85, 85, 85, 1, 1, 21, 37, 37, 37, 37, 37, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 85, 1, 2, 2, 2, 21, 21] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 39 ./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: REAL300024450302 none CCOC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 127, 127, 127, 85, 85, 85, 85, 85, 78, 41, 78, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 85, 85, 85, 85, 85, 85, 85, 41, 41, 1, 85, 85, 85, 85, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 674 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450302 none CCOC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 4, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 21, 21, 21, 31, 31, 78, 112, 201, 201, 201, 201, 201, 21, 21, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 21, 21, 21, 21, 21, 21, 21, 78, 78, 201, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 52, 26, 51] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 512 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450302 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450302 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450302/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450302 Building REAL300024450303 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450303' /scratch/stefan/7786230/working/building/REAL300024450303 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450303 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450303/0 /scratch/stefan/7786230/working/building/REAL300024450303 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/161 `/scratch/stefan/7786230/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450303/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450303 none CC1C(NC(=O)CC2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 18, 18, 9, 18, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 36, 36, 84, 126, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 18, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 84, 84, 201] 201 rigid atoms, others: [11, 38, 6, 7, 8, 9, 10, 39, 12, 45, 44, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 534 number of broken/clashed sets: 23 ./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: REAL300024450303 none CC1C(NC(=O)CC2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 89, 89, 89, 173, 201, 201, 201, 201, 201, 77, 77, 77, 66, 26, 66, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 89, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 77, 26, 26, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 764 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450303 none CC1C(NC(=O)CC2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 12, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 12, 24, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 3, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 12, 12, 77] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 211 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450303 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450303 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450303/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450303 Building REAL300024450304 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450304' /scratch/stefan/7786230/working/building/REAL300024450304 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450304 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450304/0 /scratch/stefan/7786230/working/building/REAL300024450304 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/162 `/scratch/stefan/7786230/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450304/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450304 none CC1C(NC(=O)C2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 19, 30, 51, 51, 51, 51, 51, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 19, 19, 51] 51 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 132 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: REAL300024450304 none CC1C(NC(=O)C2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 41, 41, 41, 42, 42, 42, 51, 51, 51, 51, 51, 41, 41, 41, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 42, 51, 51, 51, 51, 41, 41, 41, 41, 41, 41, 28, 28, 1] 51 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450304 none CC1C(NC(=O)C2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 11, 19, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 41] 51 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450304 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450304 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450304/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450304 Building REAL300024450305 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450305' /scratch/stefan/7786230/working/building/REAL300024450305 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450305 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450305/0 /scratch/stefan/7786230/working/building/REAL300024450305 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/163 `/scratch/stefan/7786230/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450305/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450305 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 60, 60, 60, 60, 60, 1, 1, 43, 43, 43, 43, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 187 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: REAL300024450305 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 182, 74, 74, 74, 60, 60, 60, 60, 60, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 182, 182, 74, 60, 60, 60, 60, 60, 60, 60, 30, 30, 1, 60, 60, 60, 60] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 745 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450305 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 37, 37, 37, 43, 43, 43, 43, 43, 67, 67, 96, 135, 201, 201, 201, 201, 201, 43, 43, 1, 2, 2, 2, 7, 7, 37, 43, 43, 43, 43, 43, 43, 43, 96, 96, 201, 43, 43, 43, 43] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450305 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450305 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450305/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450305 Building REAL300024450306 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450306' /scratch/stefan/7786230/working/building/REAL300024450306 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450306 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450306/0 /scratch/stefan/7786230/working/building/REAL300024450306 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/164 `/scratch/stefan/7786230/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450306/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450306 none CC1C(NC(=O)C2=NN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 21, 51, 74, 129, 129, 129, 129, 129, 15, 15, 15, 15, 15, 8, 2, 2, 2, 1, 15, 15, 15, 15, 15, 15, 51, 51, 129] 129 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 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, 44]) total number of confs: 329 number of broken/clashed sets: 22 ./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: REAL300024450306 none CC1C(NC(=O)C2=NN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [72, 72, 72, 72, 78, 78, 78, 129, 129, 129, 129, 129, 72, 72, 72, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 78, 129, 129, 129, 129, 72, 72, 72, 72, 72, 72, 38, 38, 1] 129 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 363 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450306 none CC1C(NC(=O)C2=NN(C)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 14, 1, 1, 1, 1, 1, 3, 3, 14, 26, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 14, 14, 72] 129 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450306 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450306 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450306/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450306 Building REAL300024450307 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450307' /scratch/stefan/7786230/working/building/REAL300024450307 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450307 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450307/0 /scratch/stefan/7786230/working/building/REAL300024450307 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/165 `/scratch/stefan/7786230/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450307/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450307 none CNC(=O)NCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 194, 159, 66, 66, 66, 57, 57, 57, 57, 57, 57, 26, 57, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 194, 194, 159, 159, 66, 57, 57, 57, 57, 57, 57, 57, 26, 26, 1, 57, 57, 57, 57] 201 rigid atoms, others: [46, 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, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 826 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450307 none CNC(=O)NCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 26, 26, 26, 23, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 57, 57, 57, 57, 57, 1, 1, 35, 35, 35, 35, 26, 23, 23, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 57, 1, 2, 2, 2] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450307 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450307 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450307/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450307 Building REAL300024450308 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450308' /scratch/stefan/7786230/working/building/REAL300024450308 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450308 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450308/0 /scratch/stefan/7786230/working/building/REAL300024450308 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/166 `/scratch/stefan/7786230/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(F)C=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450308/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450308 none CC1C(NC(=O)C2=C(F)C=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 21, 21, 59, 101, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 9, 1, 1, 13, 13, 13, 13, 13, 13, 59, 59, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 463 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: REAL300024450308 none CC1C(NC(=O)C2=C(F)C=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [82, 82, 82, 82, 109, 109, 109, 201, 201, 201, 201, 201, 82, 82, 82, 81, 41, 81, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 109, 201, 201, 82, 82, 82, 82, 82, 82, 41, 41, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 540 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450308 none CC1C(NC(=O)C2=C(F)C=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 15, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 29, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 3, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 82] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450308 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450308 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450308/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450308 Building REAL300024450309 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450309' /scratch/stefan/7786230/working/building/REAL300024450309 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450309 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450309/0 /scratch/stefan/7786230/working/building/REAL300024450309 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/167 `/scratch/stefan/7786230/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450309/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450309 none CCN1N=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 32, 110, 110, 110, 110, 110, 1, 1, 8, 17, 17, 17, 17, 17, 8, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 110, 1, 2, 2, 2] 159 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 244 number of broken/clashed sets: 31 ./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: REAL300024450309 none CCN1N=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [159, 134, 134, 134, 134, 132, 132, 132, 110, 110, 110, 110, 110, 102, 42, 102, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 134, 159, 159, 159, 159, 159, 134, 132, 110, 110, 110, 110, 110, 110, 110, 42, 42, 1, 110, 110, 110, 110] 159 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 579 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450309 none CCN1N=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 1, 1, 1, 1, 1, 4, 4, 3, 8, 8, 8, 8, 8, 13, 13, 37, 56, 134, 134, 134, 134, 134, 8, 8, 1, 7, 7, 7, 6, 6, 1, 4, 8, 8, 8, 8, 8, 8, 8, 37, 37, 134, 8, 8, 8, 8] 159 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 309 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450309 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450309 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450309/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450309 Building REAL300024450310 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450310' /scratch/stefan/7786230/working/building/REAL300024450310 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450310 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450310/0 /scratch/stefan/7786230/working/building/REAL300024450310 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/168 `/scratch/stefan/7786230/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450310/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450310 none CC1C(NC(=O)CC(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 29, 29, 20, 29, 8, 1, 8, 8, 1, 1, 1, 39, 39, 39, 39, 39, 51, 51, 78, 121, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 29, 20, 20, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 78, 78, 201] 201 rigid atoms, others: [43, 7, 41, 10, 11, 12, 45, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 533 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: REAL300024450310 none CC1C(NC(=O)CC(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 78, 78, 78, 114, 165, 165, 165, 201, 201, 59, 59, 59, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 78, 114, 114, 165, 165, 165, 165, 165, 165, 201, 201, 201, 201, 201, 59, 59, 59, 59, 59, 59, 29, 29, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 832 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450310 none CC1C(NC(=O)CC(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 8, 22, 22, 22, 39, 39, 1, 1, 1, 1, 1, 3, 3, 10, 16, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 4, 8, 8, 22, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 10, 10, 59] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 246 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450310 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450310 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450310/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450310 Building REAL300024450311 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450311' /scratch/stefan/7786230/working/building/REAL300024450311 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450311 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450311/0 /scratch/stefan/7786230/working/building/REAL300024450311 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/169 `/scratch/stefan/7786230/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450311/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450311 none CCN1N=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 89, 89, 89, 89, 89, 1, 1, 17, 17, 17, 17, 17, 8, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 89, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 206 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: REAL300024450311 none CCN1N=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 131, 131, 131, 131, 131, 98, 98, 98, 89, 89, 89, 89, 89, 84, 31, 84, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 131, 98, 89, 89, 89, 89, 89, 89, 89, 31, 31, 1, 89, 89, 89, 89] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 781 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450311 none CCN1N=NC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 8, 8, 8, 8, 8, 14, 14, 40, 68, 131, 131, 131, 131, 131, 8, 8, 6, 6, 6, 6, 6, 1, 6, 8, 8, 8, 8, 8, 8, 8, 40, 40, 131, 8, 8, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 323 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450311 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450311 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450311/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450311 Building REAL300024450312 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450312' /scratch/stefan/7786230/working/building/REAL300024450312 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450312 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450312/0 /scratch/stefan/7786230/working/building/REAL300024450312 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/170 `/scratch/stefan/7786230/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450312/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450312 none CC1=CSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 79, 79, 79, 79, 79, 1, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 79, 1, 2, 2, 2, 15] 127 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 25 ./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: REAL300024450312 none CC1=CSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 109, 109, 109, 79, 79, 79, 79, 79, 73, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 127, 127, 127, 127, 127, 109, 79, 79, 79, 79, 79, 79, 79, 39, 39, 1, 79, 79, 79, 79, 127] 127 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 392 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450312 none CC1=CSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 22, 22, 54, 75, 127, 127, 127, 127, 127, 15, 15, 1, 2, 2, 2, 1, 7, 15, 15, 15, 15, 15, 15, 15, 54, 54, 127, 15, 15, 15, 15, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 339 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450312 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450312 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450312/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450312 Building REAL300024450313 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450313' /scratch/stefan/7786230/working/building/REAL300024450313 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450313 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450313/0 /scratch/stefan/7786230/working/building/REAL300024450313 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/171 `/scratch/stefan/7786230/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450313/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450313 none CC1C(NC(=O)C2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 23, 23, 72, 118, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 12, 1, 1, 1, 16, 16, 16, 16, 16, 16, 72, 72, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 482 number of broken/clashed sets: 18 ./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: REAL300024450313 none CC1C(NC(=O)C2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 96, 96, 96, 201, 201, 201, 201, 91, 91, 91, 90, 43, 90, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 96, 201, 201, 201, 91, 91, 91, 91, 91, 91, 43, 43, 1] 201 rigid atoms, others: [42, 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]) total number of confs: 606 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450313 none CC1C(NC(=O)C2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 13, 30, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 3, 16, 16, 16, 1, 1, 1, 1, 1, 1, 13, 13, 91] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450313 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450313 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450313/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450313 Building REAL300024450314 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450314' /scratch/stefan/7786230/working/building/REAL300024450314 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450314 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450314/0 /scratch/stefan/7786230/working/building/REAL300024450314 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/172 `/scratch/stefan/7786230/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450314/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450314 none CCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 108, 108, 108, 72, 72, 72, 58, 58, 58, 58, 58, 57, 23, 57, 11, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 108, 108, 108, 108, 72, 58, 58, 58, 58, 58, 58, 58, 23, 23, 1, 58, 58, 58, 58] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 927 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450314 none CCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 58, 58, 58, 58, 58, 1, 1, 16, 16, 16, 16, 16, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450314 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450314 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450314/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450314 Building REAL300024450315 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450315' /scratch/stefan/7786230/working/building/REAL300024450315 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450315 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450315/0 /scratch/stefan/7786230/working/building/REAL300024450315 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/173 `/scratch/stefan/7786230/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450315/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450315 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 5, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 32, 107, 107, 107, 107, 107, 1, 1, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 107, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 212 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: REAL300024450315 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 184, 201, 201, 114, 114, 114, 107, 107, 107, 107, 107, 100, 49, 100, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 114, 107, 107, 107, 107, 107, 107, 107, 49, 49, 1, 107, 107, 107, 107] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450315 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 14, 14, 14, 14, 14, 23, 23, 64, 117, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 1, 10, 14, 14, 14, 14, 14, 14, 14, 64, 64, 201, 14, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 475 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450315 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450315 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450315/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450315 Building REAL300024450316 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450316' /scratch/stefan/7786230/working/building/REAL300024450316 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450316 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450316/0 /scratch/stefan/7786230/working/building/REAL300024450316 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/174 `/scratch/stefan/7786230/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450316/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450316 none CC(C)C#CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 161, 161, 161, 161, 161, 153, 65, 153, 13, 1, 1, 1, 1, 1, 1, 1, 161, 161, 165, 165, 165, 165, 165, 165, 165, 165, 161, 161, 161, 161, 161, 161, 161, 65, 65, 1, 161, 161, 161, 161] 165 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 492 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450316 none CC(C)C#CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 62, 161, 161, 161, 161, 161, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 161, 1, 2, 2, 2] 165 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450316 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450316 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450316/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450316 Building REAL300024450317 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450317' /scratch/stefan/7786230/working/building/REAL300024450317 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450317 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450317/0 /scratch/stefan/7786230/working/building/REAL300024450317 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/175 `/scratch/stefan/7786230/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CS1) `REAL300024450317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450317/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450317 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 62, 62, 62, 62, 62, 1, 1, 13, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 135 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: REAL300024450317 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 89, 89, 89, 62, 62, 62, 62, 62, 61, 32, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 89, 62, 62, 62, 62, 62, 62, 62, 32, 32, 1, 62, 62, 62, 62, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 469 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450317 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 13, 13, 13, 13, 13, 21, 21, 52, 93, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 52, 52, 201, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 445 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450317 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450317 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450317/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450317 Building REAL300024450318 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450318' /scratch/stefan/7786230/working/building/REAL300024450318 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450318 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450318/0 /scratch/stefan/7786230/working/building/REAL300024450318 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/176 `/scratch/stefan/7786230/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450318/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450318 none CC1C(NC(=O)CC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 38, 38, 79, 139, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 15, 5, 5, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 79, 79, 201] 603 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 556 number of broken/clashed sets: 47 ./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: REAL300024450318 none CC1C(NC(=O)CC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 104, 104, 104, 192, 201, 201, 201, 201, 76, 76, 76, 73, 28, 73, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 104, 192, 192, 603, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 28, 28, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1349 number of broken/clashed sets: 47 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450318 none CC1C(NC(=O)CC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 18, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 11, 24, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 6, 18, 18, 69, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 11, 11, 76] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 273 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450318 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450318 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450318/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450318 Building REAL300024450319 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450319' /scratch/stefan/7786230/working/building/REAL300024450319 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450319 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450319/0 /scratch/stefan/7786230/working/building/REAL300024450319 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/177 `/scratch/stefan/7786230/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450319/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450319 none CC1=CNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 54, 155, 155, 155, 155, 155, 1, 1, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 155, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 265 number of broken/clashed sets: 27 ./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: REAL300024450319 none CC1=CNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 193, 193, 155, 155, 155, 155, 155, 149, 60, 149, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 193, 155, 155, 155, 155, 155, 155, 155, 60, 60, 1, 155, 155, 155, 155] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 615 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450319 none CC1=CNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 3, 8, 8, 8, 8, 8, 14, 14, 53, 117, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 53, 53, 201, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 446 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450319 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450319 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450319/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450319 Building REAL300024450320 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450320' /scratch/stefan/7786230/working/building/REAL300024450320 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450320 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450320/0 /scratch/stefan/7786230/working/building/REAL300024450320 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/178 `/scratch/stefan/7786230/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCC1) `REAL300024450320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450320/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450320 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 90, 90, 76, 76, 76, 76, 76, 72, 38, 72, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 90, 76, 76, 76, 76, 76, 76, 76, 38, 38, 1, 76, 76, 76, 76, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 633 number of broken/clashed sets: 41 ./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: REAL300024450320 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 19, 19, 19, 19, 19, 30, 30, 86, 125, 201, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 86, 86, 201, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 535 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450320 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 23, 76, 76, 76, 76, 76, 1, 1, 19, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 76, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 21, 36, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450320 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450320 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450320/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450320 Building REAL300024450321 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450321' /scratch/stefan/7786230/working/building/REAL300024450321 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450321 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450321/0 /scratch/stefan/7786230/working/building/REAL300024450321 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/179 `/scratch/stefan/7786230/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C#CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450321/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450321 none CC1C(NC(=O)C#CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 31, 83, 166, 166, 166, 166, 166, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 31, 31, 166] 166 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 35 ./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: REAL300024450321 none CC1C(NC(=O)C#CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [164, 164, 164, 164, 166, 166, 166, 166, 166, 166, 166, 164, 164, 164, 153, 63, 153, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 166, 166, 166, 166, 166, 166, 164, 164, 164, 164, 164, 164, 63, 63, 1] 166 rigid atoms, others: [44, 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, 43]) total number of confs: 490 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450321 none CC1C(NC(=O)C#CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 17, 66, 164, 164, 164, 164, 164, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 17, 17, 164] 166 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 281 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450321 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450321 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450321/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450321 Building REAL300024450322 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450322' /scratch/stefan/7786230/working/building/REAL300024450322 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450322 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450322/0 /scratch/stefan/7786230/working/building/REAL300024450322 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/180 `/scratch/stefan/7786230/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C#CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450322/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450322 none CC1C(NC(=O)C#CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 174, 174, 174, 174, 174, 174, 174, 174, 166, 166, 166, 161, 63, 161, 13, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 166, 166, 166, 166, 166, 166, 63, 63, 1] 174 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 516 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450322 none CC1C(NC(=O)C#CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 17, 62, 166, 166, 166, 166, 166, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 17, 17, 166] 174 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 282 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450322 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450322 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450322/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450322 Building REAL300024450323 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450323' /scratch/stefan/7786230/working/building/REAL300024450323 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450323 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450323/0 /scratch/stefan/7786230/working/building/REAL300024450323 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/181 `/scratch/stefan/7786230/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450323/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450323 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [29, 29, 29, 29, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 72, 72, 72, 72, 72, 1, 1, 29, 29, 29, 29, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 72, 1, 2, 2, 2, 29] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 9 ./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: REAL300024450323 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 185, 87, 87, 87, 72, 72, 72, 72, 72, 67, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 185, 185, 87, 72, 72, 72, 72, 72, 72, 72, 27, 27, 1, 72, 72, 72, 72, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 717 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450323 none CC1=NN=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 5, 24, 24, 24, 29, 29, 29, 29, 29, 41, 41, 87, 125, 201, 201, 201, 201, 201, 29, 29, 1, 2, 2, 2, 5, 5, 24, 29, 29, 29, 29, 29, 29, 29, 87, 87, 201, 29, 29, 29, 29, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 548 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450323 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450323/1 /scratch/stefan/7786230/working/building/REAL300024450323 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/182 `/scratch/stefan/7786230/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1) `REAL300024450323.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450323/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450323 none CC1=NC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 54, 54, 54, 54, 54, 1, 1, 44, 44, 44, 44, 44, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 1, 2, 2, 2, 44] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 176 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: REAL300024450323 none CC1=NC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 166, 66, 66, 66, 54, 54, 54, 54, 54, 53, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 166, 166, 66, 54, 54, 54, 54, 54, 54, 54, 26, 26, 1, 54, 54, 54, 54, 201] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 706 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450323 none CC1=NC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 35, 35, 35, 44, 44, 44, 44, 44, 63, 63, 87, 133, 201, 201, 201, 201, 201, 44, 44, 1, 1, 2, 2, 2, 7, 7, 35, 44, 44, 44, 44, 44, 44, 44, 87, 87, 201, 44, 44, 44, 44, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 25, 26] set([5, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450323 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450323 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450323/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450323/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450323 Building REAL300024450324 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450324' /scratch/stefan/7786230/working/building/REAL300024450324 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450324 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450324/0 /scratch/stefan/7786230/working/building/REAL300024450324 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/183 `/scratch/stefan/7786230/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1) `REAL300024450324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450324/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450324 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 32, 91, 91, 91, 91, 91, 1, 1, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 91, 1, 2, 2, 2] 110 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 24 ./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: REAL300024450324 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 110, 110, 110, 110, 110, 110, 91, 91, 91, 91, 91, 83, 40, 83, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 110, 110, 110, 110, 110, 110, 110, 110, 91, 91, 91, 91, 91, 91, 91, 40, 40, 1, 91, 91, 91, 91] 110 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 357 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450324 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 15, 15, 41, 60, 110, 110, 110, 110, 110, 10, 10, 1, 1, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 41, 41, 110, 10, 10, 10, 10] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 280 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450324 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450324 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450324/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450324 Building REAL300024450325 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450325' /scratch/stefan/7786230/working/building/REAL300024450325 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450325 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450325/0 /scratch/stefan/7786230/working/building/REAL300024450325 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/184 `/scratch/stefan/7786230/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450325/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450325 none CC1C(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 53, 53, 111, 154, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 11, 1, 1, 39, 39, 39, 39, 39, 39, 111, 111, 201] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 614 number of broken/clashed sets: 86 ./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: REAL300024450325 none CC1C(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 63, 45, 63, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 113, 201, 201, 66, 66, 66, 66, 66, 66, 45, 45, 1] 201 rigid atoms, others: [44, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 662 number of broken/clashed sets: 86 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450325 none CC1C(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 39, 39, 39, 39, 39, 61, 61, 1, 1, 1, 1, 1, 3, 3, 9, 18, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 6, 39, 39, 1, 1, 1, 1, 1, 1, 9, 9, 66] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 32, 40, 41, 39, 14, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 42, 43, 44]) total number of confs: 276 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450325 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450325 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450325/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450325 Building REAL300024450326 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450326' /scratch/stefan/7786230/working/building/REAL300024450326 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450326 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450326/0 /scratch/stefan/7786230/working/building/REAL300024450326 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/185 `/scratch/stefan/7786230/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)N=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450326/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450326 none CC1=CN(C)N=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 82, 82, 82, 82, 82, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 82, 1, 2, 2, 2] 111 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 25 ./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: REAL300024450326 none CC1=CN(C)N=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 111, 111, 82, 82, 82, 82, 82, 76, 38, 76, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 111, 111, 111, 111, 111, 111, 111, 111, 82, 82, 82, 82, 82, 82, 82, 38, 38, 1, 82, 82, 82, 82] 111 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 357 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450326 none CC1=CN(C)N=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 14, 14, 43, 63, 111, 111, 111, 111, 111, 9, 9, 2, 2, 2, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 43, 43, 111, 9, 9, 9, 9] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 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, 48]) total number of confs: 297 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450326 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450326 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450326/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450326 Building REAL300024450327 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450327' /scratch/stefan/7786230/working/building/REAL300024450327 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450327 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450327/0 /scratch/stefan/7786230/working/building/REAL300024450327 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/186 `/scratch/stefan/7786230/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450327/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450327 none CC1C(NC(=O)C2CCCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 38, 38, 92, 126, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 92, 92, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 556 number of broken/clashed sets: 34 ./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: REAL300024450327 none CC1C(NC(=O)C2CCCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 96, 96, 96, 201, 201, 201, 201, 201, 201, 69, 69, 69, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 37, 37, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 632 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450327 none CC1C(NC(=O)C2CCCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 14, 22, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 14, 14, 69] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450327 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450327 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450327/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450327 Building REAL300024450328 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450328' /scratch/stefan/7786230/working/building/REAL300024450328 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450328 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450328/0 /scratch/stefan/7786230/working/building/REAL300024450328 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/187 `/scratch/stefan/7786230/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450328/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450328 none CC1C(NC(=O)CC2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 24, 24, 8, 24, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 45, 45, 85, 127, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 24, 8, 8, 2, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 85, 85, 201] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 542 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: REAL300024450328 none CC1C(NC(=O)CC2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 78, 78, 99, 99, 99, 196, 201, 201, 201, 201, 201, 78, 78, 78, 73, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 99, 196, 196, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 78, 30, 30, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 779 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450328 none CC1C(NC(=O)CC2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 4, 18, 18, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 10, 10, 78] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450328 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450328 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450328/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450328 Building REAL300024450329 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450329' /scratch/stefan/7786230/working/building/REAL300024450329 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450329 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450329/0 /scratch/stefan/7786230/working/building/REAL300024450329 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/188 `/scratch/stefan/7786230/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450329/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450329 none COCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 35, 23, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 51, 51, 51, 51, 51, 1, 1, 23, 23, 44, 44, 44, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 1, 2, 2, 2, 23, 23, 23, 23] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 244 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: REAL300024450329 none COCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 183, 141, 51, 51, 51, 51, 51, 51, 51, 51, 51, 24, 51, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 183, 183, 201, 201, 201, 201, 201, 141, 141, 51, 51, 51, 51, 51, 51, 51, 51, 24, 24, 1, 51, 51, 51, 51, 183, 183, 183, 183] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 781 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450329 none COCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 8, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 27, 27, 58, 101, 183, 183, 183, 183, 183, 23, 23, 1, 1, 15, 15, 15, 8, 8, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 58, 58, 183, 23, 23, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 49, 50, 51, 52, 25, 26] set([0, 1, 5, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450329 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450329 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450329/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450329 Building REAL300024450330 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450330' /scratch/stefan/7786230/working/building/REAL300024450330 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450330 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450330/0 /scratch/stefan/7786230/working/building/REAL300024450330 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/189 `/scratch/stefan/7786230/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450330/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450330 none CC1C(NC(=O)CCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 69, 69, 69, 156, 176, 201, 201, 201, 67, 67, 67, 67, 33, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 69, 156, 156, 176, 176, 201, 201, 201, 67, 67, 67, 67, 67, 67, 33, 33, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 805 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450330 none CC1C(NC(=O)CCNC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 23, 47, 47, 47, 1, 1, 1, 1, 1, 3, 3, 8, 17, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 3, 12, 12, 23, 23, 47, 47, 47, 1, 1, 1, 1, 1, 1, 8, 8, 67] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450330 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450330 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450330/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450330 Building REAL300024450331 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450331' /scratch/stefan/7786230/working/building/REAL300024450331 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450331 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450331/0 /scratch/stefan/7786230/working/building/REAL300024450331 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/190 `/scratch/stefan/7786230/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450331/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450331 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 24, 71, 71, 71, 71, 71, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 71, 1, 2, 2, 2, 21, 21] 193 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 35 ./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: REAL300024450331 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [193, 193, 193, 193, 97, 97, 97, 71, 71, 71, 71, 71, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 97, 71, 71, 71, 71, 71, 71, 71, 36, 36, 1, 71, 71, 71, 71, 193, 193] 193 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 609 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450331 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 32, 32, 83, 116, 193, 193, 193, 193, 193, 21, 21, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 83, 83, 193, 21, 21, 21, 21, 1, 1] 193 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 50, 51, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 537 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450331 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450331 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450331/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450331 Building REAL300024450332 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450332' /scratch/stefan/7786230/working/building/REAL300024450332 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450332 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450332/0 /scratch/stefan/7786230/working/building/REAL300024450332 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/191 `/scratch/stefan/7786230/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450332/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450332 none CCN1C=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 111, 111, 111, 111, 111, 1, 1, 10, 23, 23, 23, 23, 23, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 111, 1, 2, 2, 2] 192 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 267 number of broken/clashed sets: 41 ./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: REAL300024450332 none CCN1C=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 150, 150, 150, 150, 149, 149, 149, 111, 111, 111, 111, 111, 100, 41, 100, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 150, 192, 192, 192, 192, 192, 150, 150, 149, 111, 111, 111, 111, 111, 111, 111, 41, 41, 1, 111, 111, 111, 111] 192 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 728 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450332 none CCN1C=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 17, 17, 42, 63, 150, 150, 150, 150, 150, 10, 10, 1, 8, 8, 8, 8, 8, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 42, 42, 150, 10, 10, 10, 10] 192 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 353 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450332 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450332 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450332/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450332 Building REAL300024450333 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450333' /scratch/stefan/7786230/working/building/REAL300024450333 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450333 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450333/0 /scratch/stefan/7786230/working/building/REAL300024450333 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/192 `/scratch/stefan/7786230/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450333/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450333 none CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 161, 161, 94, 94, 94, 68, 68, 68, 68, 68, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 161, 201, 201, 161, 161, 161, 161, 161, 161, 94, 68, 68, 68, 68, 68, 68, 68, 37, 37, 1, 68, 68, 68, 68, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 896 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450333 none CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 68, 68, 68, 68, 68, 1, 1, 11, 19, 19, 12, 12, 12, 12, 12, 11, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 68, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450333 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450333 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450333/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450333 Building REAL300024450334 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450334' /scratch/stefan/7786230/working/building/REAL300024450334 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450334 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450334/0 /scratch/stefan/7786230/working/building/REAL300024450334 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/193 `/scratch/stefan/7786230/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450334/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450334 none C#CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 132, 132, 57, 57, 57, 42, 42, 42, 42, 42, 41, 22, 41, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 201, 201, 201, 132, 132, 132, 132, 57, 42, 42, 42, 42, 42, 42, 42, 22, 22, 1, 42, 42, 42, 42] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 844 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450334 none C#CCOCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 42, 22, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 42, 42, 42, 42, 42, 1, 1, 42, 42, 42, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450334 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450334 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450334/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450334 Building REAL300024450335 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450335' /scratch/stefan/7786230/working/building/REAL300024450335 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450335 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450335/0 /scratch/stefan/7786230/working/building/REAL300024450335 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/194 `/scratch/stefan/7786230/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450335/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450335 none C#CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 168, 159, 89, 159, 89, 89, 72, 72, 72, 72, 72, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 159, 159, 159, 159, 89, 72, 72, 72, 72, 72, 72, 72, 29, 29, 1, 72, 72, 72, 72] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 810 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450335 none C#CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 23, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 72, 72, 72, 72, 72, 1, 1, 44, 44, 44, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 72, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 285 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450335 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450335 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450335/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450335 Building REAL300024450336 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450336' /scratch/stefan/7786230/working/building/REAL300024450336 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450336 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450336/0 /scratch/stefan/7786230/working/building/REAL300024450336 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/195 `/scratch/stefan/7786230/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCOCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450336/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450336 none CC1C(NC(=O)CCOCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 70, 70, 37, 70, 26, 18, 6, 1, 1, 1, 1, 76, 76, 76, 76, 76, 79, 79, 86, 124, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 70, 37, 37, 26, 26, 6, 6, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 86, 86, 201] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 510 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: REAL300024450336 none CC1C(NC(=O)CCOCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 28, 28, 36, 36, 36, 114, 118, 133, 189, 201, 201, 28, 28, 28, 28, 25, 28, 12, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 36, 114, 114, 118, 118, 189, 189, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 28, 25, 25, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 829 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450336 none CC1C(NC(=O)CCOCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 16, 26, 49, 76, 76, 1, 1, 1, 1, 1, 3, 3, 5, 8, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 3, 13, 13, 16, 16, 49, 49, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 5, 5, 28] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450336 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450336 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450336/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450336 Building REAL300024450337 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450337' /scratch/stefan/7786230/working/building/REAL300024450337 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450337 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450337/0 /scratch/stefan/7786230/working/building/REAL300024450337 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/196 `/scratch/stefan/7786230/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450337/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450337 none CC1C(NC(=O)COC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 38, 38, 13, 38, 5, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 57, 57, 96, 134, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 38, 13, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 96, 96, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 567 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: REAL300024450337 none CC1C(NC(=O)COC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 78, 78, 78, 152, 193, 201, 201, 201, 201, 69, 69, 69, 68, 25, 68, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 78, 152, 152, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 25, 25, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 672 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450337 none CC1C(NC(=O)COC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 27, 43, 43, 43, 43, 1, 1, 1, 1, 1, 3, 3, 11, 20, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 3, 11, 11, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 11, 11, 69] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 242 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450337 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450337 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450337/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450337 Building REAL300024450338 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450338' /scratch/stefan/7786230/working/building/REAL300024450338 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450338 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450338/0 /scratch/stefan/7786230/working/building/REAL300024450338 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/197 `/scratch/stefan/7786230/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)NC(N)=O) `REAL300024450338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450338/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450338 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 189, 96, 96, 96, 73, 73, 73, 73, 73, 70, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 96, 73, 73, 73, 73, 73, 73, 73, 29, 29, 1, 73, 73, 73, 73, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 773 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450338 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 73, 73, 73, 73, 73, 1, 1, 28, 35, 35, 35, 28, 28, 28, 28, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 73, 1, 2, 2, 2, 35, 35, 35] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 11, 40, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 279 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450338 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450338 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450338/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450338 Building REAL300024450339 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450339' /scratch/stefan/7786230/working/building/REAL300024450339 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450339 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450339/0 /scratch/stefan/7786230/working/building/REAL300024450339 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/198 `/scratch/stefan/7786230/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C(F)F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450339/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450339 none CC1C(NC(=O)C2(C(F)F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 7, 7, 1, 7, 1, 1, 9, 9, 1, 1, 25, 25, 25, 25, 25, 37, 37, 80, 120, 182, 182, 182, 182, 182, 25, 25, 25, 25, 25, 7, 9, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 80, 80, 182] 193 rigid atoms, others: [33, 34, 35, 4, 6, 7, 10, 11, 36] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 525 number of broken/clashed sets: 90 ./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: REAL300024450339 none CC1C(NC(=O)C2(C(F)F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 95, 95, 95, 182, 193, 193, 182, 182, 60, 60, 60, 57, 42, 57, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 95, 193, 182, 182, 182, 182, 60, 60, 60, 60, 60, 60, 42, 42, 1] 193 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 662 number of broken/clashed sets: 90 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450339 none CC1C(NC(=O)C2(C(F)F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 25, 49, 49, 25, 25, 1, 1, 1, 1, 1, 3, 3, 9, 18, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 6, 49, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 9, 9, 60] 193 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 279 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450339 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450339 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450339/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450339 Building REAL300024450340 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450340' /scratch/stefan/7786230/working/building/REAL300024450340 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450340 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450340/0 /scratch/stefan/7786230/working/building/REAL300024450340 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/199 `/scratch/stefan/7786230/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450340/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450340 none C=CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 75, 156, 156, 75, 75, 55, 55, 55, 55, 55, 53, 26, 53, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 75, 55, 55, 55, 55, 55, 55, 55, 26, 26, 1, 55, 55, 55, 55] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 900 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450340 none C=CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 55, 55, 55, 55, 55, 1, 1, 29, 29, 29, 22, 22, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450340 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450340 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450340/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450340 Building REAL300024450341 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450341' /scratch/stefan/7786230/working/building/REAL300024450341 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450341 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450341/0 /scratch/stefan/7786230/working/building/REAL300024450341 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/200 `/scratch/stefan/7786230/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC23CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450341/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450341 none CC1C(NC(=O)C2CC23CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 42, 42, 90, 126, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 90, 90, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 553 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: REAL300024450341 none CC1C(NC(=O)C2CC23CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 94, 94, 94, 201, 201, 201, 201, 201, 70, 70, 70, 66, 37, 66, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 37, 37, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 636 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450341 none CC1C(NC(=O)C2CC23CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 12, 20, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 12, 12, 70] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450341 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450341 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450341/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450341 Building REAL300024450342 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450342' /scratch/stefan/7786230/working/building/REAL300024450342 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450342 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450342/0 /scratch/stefan/7786230/working/building/REAL300024450342 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/201 `/scratch/stefan/7786230/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450342/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450342 none CC1=CC=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 24, 24, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 84, 84, 84, 84, 84, 1, 1, 24, 24, 24, 24, 24, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 84, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 205 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: REAL300024450342 none CC1=CC=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 112, 112, 112, 84, 84, 84, 84, 84, 81, 29, 81, 12, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 112, 84, 84, 84, 84, 84, 84, 84, 29, 29, 1, 84, 84, 84, 84] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 811 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450342 none CC1=CC=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 16, 16, 16, 24, 24, 24, 24, 24, 38, 38, 83, 126, 201, 201, 201, 201, 201, 24, 24, 2, 2, 2, 1, 1, 5, 5, 16, 24, 24, 24, 24, 24, 24, 24, 83, 83, 201, 24, 24, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 549 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450342 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450342 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450342/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450342 Building REAL300024450343 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450343' /scratch/stefan/7786230/working/building/REAL300024450343 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450343 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450343/0 /scratch/stefan/7786230/working/building/REAL300024450343 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/202 `/scratch/stefan/7786230/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1) `REAL300024450343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450343/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450343 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 95, 95, 95, 95, 95, 1, 1, 16, 16, 16, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 95, 1, 2, 2, 2, 16] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 239 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: REAL300024450343 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 194, 194, 129, 129, 129, 95, 95, 95, 95, 95, 89, 29, 89, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 194, 194, 194, 201, 201, 201, 201, 201, 129, 95, 95, 95, 95, 95, 95, 95, 29, 29, 1, 95, 95, 95, 95, 194] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450343 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 16, 16, 16, 16, 16, 25, 25, 60, 98, 194, 194, 194, 194, 194, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 10, 16, 16, 16, 16, 16, 16, 16, 60, 60, 194, 16, 16, 16, 16, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450343 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450343 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450343/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450343 Building REAL300024450344 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450344' /scratch/stefan/7786230/working/building/REAL300024450344 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450344 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450344/0 /scratch/stefan/7786230/working/building/REAL300024450344 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/203 `/scratch/stefan/7786230/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450344/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450344 none CC1C(NC(=O)CC2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 42, 42, 86, 129, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 20, 5, 5, 1, 1, 28, 28, 28, 28, 28, 28, 86, 86, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 539 number of broken/clashed sets: 7 ./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: REAL300024450344 none CC1C(NC(=O)CC2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 113, 113, 113, 193, 201, 201, 201, 201, 84, 84, 84, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 113, 193, 193, 201, 201, 84, 84, 84, 84, 84, 84, 29, 29, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 780 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450344 none CC1C(NC(=O)CC2=CSC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 10, 18, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 4, 20, 20, 28, 28, 1, 1, 1, 1, 1, 1, 10, 10, 84] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450344 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450344 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450344/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450344 Building REAL300024450345 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450345' /scratch/stefan/7786230/working/building/REAL300024450345 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450345 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450345/0 /scratch/stefan/7786230/working/building/REAL300024450345 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/204 `/scratch/stefan/7786230/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450345/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450345 none CC1C(NC(=O)CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 112, 112, 112, 198, 201, 201, 201, 201, 80, 80, 80, 77, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 112, 198, 198, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 80, 30, 30, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 787 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450345 none CC1C(NC(=O)CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 10, 18, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 3, 17, 17, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 10, 10, 80] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 242 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450345 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450345 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450345/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450345 Building REAL300024450346 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450346' /scratch/stefan/7786230/working/building/REAL300024450346 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450346 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450346/0 /scratch/stefan/7786230/working/building/REAL300024450346 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/205 `/scratch/stefan/7786230/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450346/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450346 none CC1C(NC(=O)C2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 34, 51, 93, 93, 93, 93, 93, 10, 10, 10, 10, 10, 4, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 34, 34, 93] 93 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 44, 45]) total number of confs: 230 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: REAL300024450346 none CC1C(NC(=O)C2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 93, 93, 93, 93, 93, 93, 93, 93, 79, 79, 79, 75, 39, 75, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 93, 93, 93, 93, 93, 93, 79, 79, 79, 79, 79, 79, 39, 39, 1] 93 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 310 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450346 none CC1C(NC(=O)C2=NN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 16, 30, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 79] 93 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450346 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450346 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450346/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450346 Building REAL300024450347 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450347' /scratch/stefan/7786230/working/building/REAL300024450347 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450347 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450347/0 /scratch/stefan/7786230/working/building/REAL300024450347 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/206 `/scratch/stefan/7786230/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450347/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450347 none CC1=NC=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 41, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 56, 56, 56, 56, 56, 1, 1, 41, 41, 41, 41, 41, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 197 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: REAL300024450347 none CC1=NC=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 169, 69, 69, 69, 56, 56, 56, 56, 56, 55, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 169, 169, 69, 56, 56, 56, 56, 56, 56, 56, 27, 27, 1, 56, 56, 56, 56] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 706 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450347 none CC1=NC=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 29, 29, 29, 41, 41, 41, 41, 41, 58, 58, 88, 130, 201, 201, 201, 201, 201, 41, 41, 2, 2, 2, 1, 1, 7, 7, 29, 41, 41, 41, 41, 41, 41, 41, 88, 88, 201, 41, 41, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450347 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450347/1 /scratch/stefan/7786230/working/building/REAL300024450347 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/207 `/scratch/stefan/7786230/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450347.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450347/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450347 none CC1=[NH+]C=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 28, 28, 28, 28, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 15, 55, 55, 55, 55, 55, 1, 1, 28, 28, 28, 28, 28, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 55, 1, 2, 2, 2] 113 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 27 ./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: REAL300024450347 none CC1=[NH+]C=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 94, 62, 62, 62, 55, 55, 55, 55, 55, 45, 27, 45, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 113, 113, 113, 113, 113, 94, 94, 62, 55, 55, 55, 55, 55, 55, 55, 27, 27, 1, 55, 55, 55, 55] 113 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 398 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450347 none CC1=[NH+]C=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 28, 28, 28, 28, 28, 28, 28, 53, 74, 113, 113, 113, 113, 113, 28, 28, 2, 2, 2, 1, 1, 4, 4, 21, 28, 28, 28, 28, 28, 28, 28, 53, 53, 113, 28, 28, 28, 28] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450347 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450347 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450347/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450347/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450347 Building REAL300024450348 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450348' /scratch/stefan/7786230/working/building/REAL300024450348 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450348 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450348/0 /scratch/stefan/7786230/working/building/REAL300024450348 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/208 `/scratch/stefan/7786230/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450348/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450348 none CCN1C=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 10, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 86, 86, 86, 86, 86, 1, 1, 17, 17, 17, 17, 17, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 24 ./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: REAL300024450348 none CCN1C=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 130, 130, 130, 130, 130, 100, 100, 100, 86, 86, 86, 86, 86, 79, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 130, 130, 130, 100, 86, 86, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86, 86, 86] 201 rigid atoms, others: [45, 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, 43, 44, 46, 47, 48, 49]) total number of confs: 797 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450348 none CCN1C=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 15, 15, 42, 70, 130, 130, 130, 130, 130, 10, 10, 5, 5, 5, 5, 5, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 10, 42, 42, 130, 10, 10, 10, 10] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34] set([0, 8, 9, 10, 11, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450348 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450348 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450348/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450348 Building REAL300024450349 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450349' /scratch/stefan/7786230/working/building/REAL300024450349 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450349 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450349/0 /scratch/stefan/7786230/working/building/REAL300024450349 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/209 `/scratch/stefan/7786230/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450349/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450349 none CC1C(NC(=O)CC2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 28, 28, 9, 28, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 48, 48, 79, 120, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 79, 79, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 513 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: REAL300024450349 none CC1C(NC(=O)CC2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 94, 94, 94, 185, 201, 201, 201, 201, 201, 72, 72, 72, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 94, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 72, 72, 30, 30, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 764 number of broken/clashed sets: 4 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450349 none CC1C(NC(=O)CC2CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 3, 3, 10, 17, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 4, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 10, 10, 72] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450349 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450349 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450349/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450349 Building REAL300024450350 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450350' /scratch/stefan/7786230/working/building/REAL300024450350 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450350 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450350/0 /scratch/stefan/7786230/working/building/REAL300024450350 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/210 `/scratch/stefan/7786230/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450350/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450350 none CC1C(NC(=O)C2CCC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 22, 22, 78, 119, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 78, 78, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 506 number of broken/clashed sets: 39 ./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: REAL300024450350 none CC1C(NC(=O)C2CCC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 104, 104, 104, 201, 201, 201, 201, 201, 201, 91, 91, 91, 85, 42, 85, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 42, 42, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 641 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450350 none CC1C(NC(=O)C2CCC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 13, 28, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 13, 13, 91] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450350 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450350 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450350/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450350 Building REAL300024450351 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450351' /scratch/stefan/7786230/working/building/REAL300024450351 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450351 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450351/0 /scratch/stefan/7786230/working/building/REAL300024450351 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/211 `/scratch/stefan/7786230/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450351/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450351 none CC1=NC=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 33, 76, 76, 76, 76, 76, 1, 1, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 76, 1, 2, 2, 2] 95 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 23 ./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: REAL300024450351 none CC1=NC=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 95, 95, 95, 95, 91, 91, 91, 76, 76, 76, 76, 76, 70, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 95, 95, 95, 95, 95, 95, 91, 76, 76, 76, 76, 76, 76, 76, 37, 37, 1, 76, 76, 76, 76] 95 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 308 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450351 none CC1=NC=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 11, 11, 37, 58, 95, 95, 95, 95, 95, 8, 8, 1, 2, 2, 2, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 37, 37, 95, 8, 8, 8, 8] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450351 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450351 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450351/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450351 Building REAL300024450352 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450352' /scratch/stefan/7786230/working/building/REAL300024450352 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450352 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450352/0 /scratch/stefan/7786230/working/building/REAL300024450352 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/212 `/scratch/stefan/7786230/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450352/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450352 none COCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 176, 101, 176, 101, 101, 81, 81, 81, 81, 81, 78, 29, 78, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 179, 179, 176, 176, 176, 176, 101, 81, 81, 81, 81, 81, 81, 81, 29, 29, 1, 81, 81, 81, 81] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 832 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450352 none COCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 17, 11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 81, 81, 81, 81, 81, 1, 1, 33, 33, 33, 22, 22, 17, 17, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 81, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 248 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450352 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450352 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450352/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450352 Building REAL300024450353 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450353' /scratch/stefan/7786230/working/building/REAL300024450353 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450353 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450353/0 /scratch/stefan/7786230/working/building/REAL300024450353 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/213 `/scratch/stefan/7786230/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450353/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450353 none CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 191, 191, 157, 157, 157, 113, 113, 113, 113, 113, 113, 41, 113, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 191, 201, 201, 191, 191, 191, 191, 191, 191, 157, 113, 113, 113, 113, 113, 113, 113, 41, 41, 1, 113, 113, 113, 113, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 713 number of broken/clashed sets: 14 ./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: REAL300024450353 none CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 6, 1, 6, 17, 17, 17, 27, 27, 27, 27, 27, 37, 37, 73, 105, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 6, 17, 27, 27, 27, 27, 27, 27, 27, 73, 73, 201, 27, 27, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 493 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450353 none CCOC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 113, 113, 113, 113, 113, 1, 1, 15, 27, 27, 18, 18, 18, 18, 18, 15, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 113, 1, 2, 2, 2, 27, 27, 27, 27, 27] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450353 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450353 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450353/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450353 Building REAL300024450354 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450354' /scratch/stefan/7786230/working/building/REAL300024450354 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450354 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450354/0 /scratch/stefan/7786230/working/building/REAL300024450354 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/214 `/scratch/stefan/7786230/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2N=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450354/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450354 none CC1C(NC(=O)CN2N=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 8, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 36, 36, 8, 36, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 52, 52, 96, 133, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 36, 8, 8, 1, 39, 39, 39, 39, 39, 39, 96, 96, 201] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 563 number of broken/clashed sets: 7 ./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: REAL300024450354 none CC1C(NC(=O)CN2N=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 8, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 69, 69, 69, 169, 201, 201, 201, 201, 68, 68, 68, 63, 24, 63, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 69, 169, 169, 201, 68, 68, 68, 68, 68, 68, 24, 24, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 677 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450354 none CC1C(NC(=O)CN2N=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 8, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 11, 20, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 3, 14, 14, 39, 1, 1, 1, 1, 1, 1, 11, 11, 68] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450354 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450354 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450354/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450354 Building REAL300024450355 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450355' /scratch/stefan/7786230/working/building/REAL300024450355 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450355 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450355/0 /scratch/stefan/7786230/working/building/REAL300024450355 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/215 `/scratch/stefan/7786230/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450355/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450355 none CCCC[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 165, 73, 165, 165, 73, 73, 59, 59, 59, 59, 59, 56, 23, 56, 11, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 73, 59, 59, 59, 59, 59, 59, 59, 23, 23, 1, 59, 59, 59, 59] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 844 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450355 none CCCC[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 27, 26, 14, 3, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 59, 59, 59, 59, 59, 1, 1, 29, 29, 29, 29, 29, 27, 27, 27, 27, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 59, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 249 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450355 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450355 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450355/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450355 Building REAL300024450356 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450356' /scratch/stefan/7786230/working/building/REAL300024450356 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450356 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450356/0 /scratch/stefan/7786230/working/building/REAL300024450356 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/216 `/scratch/stefan/7786230/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450356/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450356 none C=CCC(CC=C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 151, 125, 68, 125, 166, 194, 68, 68, 50, 50, 50, 50, 50, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 179, 179, 179, 151, 151, 125, 166, 166, 194, 194, 194, 68, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 50, 50, 50, 50] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 1101 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450356 none C=CCC(CC=C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 10, 3, 10, 17, 31, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 50, 50, 50, 50, 50, 1, 1, 27, 27, 27, 17, 17, 10, 17, 17, 31, 31, 31, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 271 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450356 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450356 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450356/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450356 Building REAL300024450357 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450357' /scratch/stefan/7786230/working/building/REAL300024450357 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450357 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450357/0 /scratch/stefan/7786230/working/building/REAL300024450357 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/217 `/scratch/stefan/7786230/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450357/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450357 none CC1C(NC(=O)C2(C)CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 33, 100, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 33, 33, 201] 201 rigid atoms, others: [43, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 383 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: REAL300024450357 none CC1C(NC(=O)C2(C)CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 181, 181, 183, 183, 183, 201, 201, 201, 201, 201, 201, 181, 181, 181, 173, 67, 173, 13, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 181, 181, 67, 67, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 612 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450357 none CC1C(NC(=O)C2(C)CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 17, 55, 181, 181, 181, 181, 181, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 17, 17, 181] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450357 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450357 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450357/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450357 Building REAL300024450358 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450358' /scratch/stefan/7786230/working/building/REAL300024450358 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450358 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450358/0 /scratch/stefan/7786230/working/building/REAL300024450358 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/218 `/scratch/stefan/7786230/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450358/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450358 none CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 127, 201, 201, 58, 58, 58, 47, 47, 47, 47, 47, 46, 25, 46, 12, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 58, 47, 47, 47, 47, 47, 47, 47, 25, 25, 1, 47, 47, 47, 47] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 837 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450358 none CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 27, 9, 27, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 47, 47, 47, 47, 47, 1, 1, 37, 37, 37, 37, 37, 27, 27, 27, 27, 27, 27, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 47, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450358 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450358 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450358/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450358 Building REAL300024450359 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450359' /scratch/stefan/7786230/working/building/REAL300024450359 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450359 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450359/0 /scratch/stefan/7786230/working/building/REAL300024450359 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/219 `/scratch/stefan/7786230/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450359/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450359 none CC(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 181, 181, 98, 181, 181, 98, 98, 61, 61, 61, 61, 61, 59, 41, 59, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 98, 61, 61, 61, 61, 61, 61, 61, 41, 41, 1, 61, 61, 61, 61] 181 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 790 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450359 none CC(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 61, 61, 61, 61, 61, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 61, 1, 2, 2, 2] 181 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 172 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450359 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450359 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450359/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450359 Building REAL300024450360 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450360' /scratch/stefan/7786230/working/building/REAL300024450360 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450360 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450360/0 /scratch/stefan/7786230/working/building/REAL300024450360 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/220 `/scratch/stefan/7786230/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450360/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450360 none C=CC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 149, 201, 201, 84, 84, 84, 64, 64, 64, 64, 64, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 84, 64, 64, 64, 64, 64, 64, 64, 29, 29, 1, 64, 64, 64, 64] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 864 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450360 none C=CC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 12, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 64, 64, 64, 64, 64, 1, 1, 33, 33, 33, 26, 26, 26, 26, 26, 26, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450360 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450360 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450360/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450360 Building REAL300024450361 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450361' /scratch/stefan/7786230/working/building/REAL300024450361 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450361 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450361/0 /scratch/stefan/7786230/working/building/REAL300024450361 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/221 `/scratch/stefan/7786230/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2N=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450361/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450361 none CC1C(NC(=O)CN2N=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 25, 25, 5, 25, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 48, 48, 93, 130, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 25, 5, 5, 1, 1, 32, 32, 32, 32, 32, 32, 93, 93, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 560 number of broken/clashed sets: 7 ./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: REAL300024450361 none CC1C(NC(=O)CN2N=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 87, 87, 87, 115, 115, 115, 201, 201, 201, 201, 201, 87, 87, 87, 84, 31, 84, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 115, 201, 201, 201, 201, 87, 87, 87, 87, 87, 87, 31, 31, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 788 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450361 none CC1C(NC(=O)CN2N=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 20, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 10, 18, 87, 87, 87, 87, 87, 2, 2, 2, 1, 1, 5, 20, 20, 39, 39, 1, 1, 1, 1, 1, 1, 10, 10, 87] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450361 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450361 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450361/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450361 Building REAL300024450362 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450362' /scratch/stefan/7786230/working/building/REAL300024450362 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450362 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450362/0 /scratch/stefan/7786230/working/building/REAL300024450362 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/222 `/scratch/stefan/7786230/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450362/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450362 none CC1C(NC(=O)CCC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 22, 22, 8, 22, 4, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 38, 38, 81, 112, 170, 170, 170, 170, 170, 26, 26, 26, 26, 26, 22, 8, 8, 4, 4, 1, 1, 1, 26, 26, 26, 26, 26, 26, 81, 81, 170] 170 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 475 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: REAL300024450362 none CC1C(NC(=O)CCC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 53, 53, 58, 58, 58, 162, 177, 177, 177, 177, 177, 53, 53, 53, 53, 31, 53, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 58, 162, 162, 177, 177, 177, 177, 177, 53, 53, 53, 53, 53, 53, 31, 31, 1] 177 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 707 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450362 none CC1C(NC(=O)CCC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 20, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 11, 19, 53, 53, 53, 53, 53, 2, 2, 2, 1, 1, 3, 12, 12, 20, 20, 29, 29, 29, 1, 1, 1, 1, 1, 1, 11, 11, 53] 177 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450362 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450362 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450362/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450362 Building REAL300024450363 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450363' /scratch/stefan/7786230/working/building/REAL300024450363 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450363 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450363/0 /scratch/stefan/7786230/working/building/REAL300024450363 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/223 `/scratch/stefan/7786230/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450363/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450363 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 17, 17, 51, 86, 189, 189, 189, 189, 189, 14, 14, 14, 14, 14, 11, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 51, 51, 189] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 428 number of broken/clashed sets: 32 ./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.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: REAL300024450363 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 66, 66, 66, 189, 189, 189, 189, 189, 201, 201, 60, 60, 60, 56, 38, 56, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 66, 189, 189, 201, 201, 201, 201, 201, 60, 60, 60, 60, 60, 60, 38, 38, 1] 201 rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 609 number of broken/clashed sets: 32 ./output.4.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: REAL300024450363 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 42, 42, 5, 42, 5, 5, 5, 1, 5, 1, 1, 1, 46, 46, 46, 46, 46, 50, 50, 100, 136, 201, 201, 201, 201, 201, 46, 46, 46, 46, 46, 42, 5, 5, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 100, 100, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 544 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450363 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 46, 46, 1, 1, 1, 1, 1, 3, 3, 8, 14, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 3, 14, 14, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 8, 8, 60] 201 rigid atoms, others: [0, 1, 2, 3, 32, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 46, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 219 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450363 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450363 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450363/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450363 Building REAL300024450364 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450364' /scratch/stefan/7786230/working/building/REAL300024450364 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450364 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450364/0 /scratch/stefan/7786230/working/building/REAL300024450364 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/224 `/scratch/stefan/7786230/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]2C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450364/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450364 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 22, 22, 22, 22, 31, 31, 71, 109, 185, 185, 185, 185, 185, 22, 22, 22, 22, 22, 12, 1, 1, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 71, 71, 185] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 479 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.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: REAL300024450364 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 57, 57, 76, 76, 76, 185, 185, 185, 185, 185, 201, 201, 201, 57, 57, 57, 53, 33, 53, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 76, 185, 185, 201, 201, 201, 201, 201, 201, 201, 57, 57, 57, 57, 57, 57, 33, 33, 1] 201 rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 634 number of broken/clashed sets: 37 ./output.4.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: REAL300024450364 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 28, 28, 4, 28, 4, 4, 4, 1, 4, 1, 1, 1, 1, 38, 38, 38, 38, 38, 47, 47, 95, 133, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 28, 4, 4, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 95, 95, 201] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 545 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450364 none CC1C(NC(=O)[C@@H]2C[C@H]2C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 22, 22, 22, 22, 22, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 9, 16, 57, 57, 57, 57, 57, 2, 2, 2, 1, 1, 5, 22, 22, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 9, 9, 57] 201 rigid atoms, others: [0, 1, 2, 3, 48, 33, 32, 44, 45, 46, 15, 16, 17, 18, 19, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450364 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450364 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450364/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450364 Building REAL300024450365 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450365' /scratch/stefan/7786230/working/building/REAL300024450365 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450365 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450365/0 /scratch/stefan/7786230/working/building/REAL300024450365 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/225 `/scratch/stefan/7786230/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@@H+]1C) `REAL300024450365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450365/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 50, 50, 50, 50, 50, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9] 76 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 76 ./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: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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, 76, 68, 76, 68, 68, 50, 50, 50, 50, 50, 48, 31, 48, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 76, 76, 76, 76, 76, 76, 76, 76, 68, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 50, 50, 50, 50, 76, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 261 number of broken/clashed sets: 76 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 15, 15, 39, 50, 76, 76, 76, 76, 76, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 39, 39, 76, 9, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 50, 51, 25, 26, 27, 28, 29] set([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, 52, 53, 54]) total number of confs: 237 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450365 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450365/1 /scratch/stefan/7786230/working/building/REAL300024450365 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/226 `/scratch/stefan/7786230/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@H+]1C) `REAL300024450365.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450365/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 27 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: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 11 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450365 none C[C@@H]1[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 50, 51, 25, 26, 27, 28, 29] set([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, 52, 53, 54]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450365 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450365 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450365/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450365/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450365 Building REAL300024450366 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450366' /scratch/stefan/7786230/working/building/REAL300024450366 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450366 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450366/0 /scratch/stefan/7786230/working/building/REAL300024450366 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/227 `/scratch/stefan/7786230/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450366/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450366 none CCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [154, 150, 110, 150, 150, 154, 110, 110, 79, 79, 79, 79, 79, 77, 55, 77, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 160, 160, 160, 160, 160, 150, 150, 150, 160, 160, 160, 160, 160, 110, 79, 79, 79, 79, 79, 79, 79, 55, 55, 1, 79, 79, 79, 79] 160 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 763 number of broken/clashed sets: 60 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450366 none CCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [17, 16, 6, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 79, 79, 79, 79, 79, 1, 1, 20, 20, 20, 20, 20, 16, 16, 16, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 79, 1, 2, 2, 2] 160 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 274 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450366 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450366 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450366/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450366 Building REAL300024450367 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450367' /scratch/stefan/7786230/working/building/REAL300024450367 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450367 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450367/0 /scratch/stefan/7786230/working/building/REAL300024450367 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/228 `/scratch/stefan/7786230/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C=CC=CC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450367/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450367 none CC1C(NC(=O)C2C=CC=CC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 47, 78, 144, 144, 144, 144, 144, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 47, 47, 144] 144 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 342 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: REAL300024450367 none CC1C(NC(=O)C2C=CC=CC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 130, 130, 130, 144, 144, 144, 144, 144, 144, 98, 98, 98, 89, 42, 89, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 130, 144, 144, 144, 144, 144, 144, 144, 98, 98, 98, 98, 98, 98, 42, 42, 1] 144 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 495 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450367 none CC1C(NC(=O)C2C=CC=CC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 27, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 98] 144 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450367 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450367 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450367/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450367 Building REAL300024450368 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450368' /scratch/stefan/7786230/working/building/REAL300024450368 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450368 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450368/0 /scratch/stefan/7786230/working/building/REAL300024450368 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/229 `/scratch/stefan/7786230/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450368/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450368 none C=C(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 199, 79, 79, 79, 65, 65, 65, 65, 65, 61, 25, 61, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 199, 199, 79, 65, 65, 65, 65, 65, 65, 65, 25, 25, 1, 65, 65, 65, 65] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 754 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450368 none C=C(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 36, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 65, 65, 65, 65, 65, 1, 1, 36, 36, 36, 36, 36, 22, 22, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450368 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450368 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450368/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450368 Building REAL300024450369 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450369' /scratch/stefan/7786230/working/building/REAL300024450369 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450369 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450369/0 /scratch/stefan/7786230/working/building/REAL300024450369 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/230 `/scratch/stefan/7786230/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450369/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450369 none CC1C(NC(=O)C2=CC=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 20, 20, 50, 103, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 7, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 23 ./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: REAL300024450369 none CC1C(NC(=O)C2=CC=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [135, 135, 135, 135, 137, 137, 137, 201, 201, 201, 201, 135, 135, 135, 135, 59, 135, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 137, 201, 201, 135, 135, 135, 135, 135, 135, 59, 59, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 550 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450369 none CC1C(NC(=O)C2=CC=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 14, 46, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 4, 13, 13, 1, 1, 1, 1, 1, 1, 14, 14, 135] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450369 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450369 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450369/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450369 Building REAL300024450370 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450370' /scratch/stefan/7786230/working/building/REAL300024450370 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450370 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450370/0 /scratch/stefan/7786230/working/building/REAL300024450370 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/231 `/scratch/stefan/7786230/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450370/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450370 none CCC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 28, 119, 119, 119, 119, 119, 1, 1, 15, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 119, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 286 number of broken/clashed sets: 32 ./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: REAL300024450370 none CCC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 139, 139, 139, 119, 119, 119, 119, 119, 112, 42, 112, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 119, 119, 119, 119, 119, 119, 119, 42, 42, 1, 119, 119, 119, 119] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 637 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450370 none CCC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 15, 15, 15, 15, 15, 23, 23, 72, 101, 201, 201, 201, 201, 201, 15, 15, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 72, 72, 201, 15, 15, 15, 15] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 36, 26, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 476 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450370 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450370 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450370/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450370 Building REAL300024450371 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450371' /scratch/stefan/7786230/working/building/REAL300024450371 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450371 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450371/0 /scratch/stefan/7786230/working/building/REAL300024450371 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/232 `/scratch/stefan/7786230/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450371/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450371 none COCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 22, 16, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 61, 61, 61, 61, 61, 1, 1, 12, 12, 29, 29, 29, 22, 22, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 1, 2, 2, 2, 12, 12, 12, 12] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 205 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: REAL300024450371 none COCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 178, 79, 79, 79, 61, 61, 61, 61, 61, 60, 26, 60, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 178, 178, 201, 201, 201, 201, 201, 189, 189, 79, 61, 61, 61, 61, 61, 61, 61, 26, 26, 1, 61, 61, 61, 61, 178, 178, 178, 178] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 663 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450371 none COCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 4, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 20, 20, 45, 81, 178, 178, 178, 178, 178, 12, 12, 1, 1, 16, 16, 16, 7, 7, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 45, 45, 178, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 439 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450371 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450371 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450371/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450371 Building REAL300024450372 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450372' /scratch/stefan/7786230/working/building/REAL300024450372 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450372 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450372/0 /scratch/stefan/7786230/working/building/REAL300024450372 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/233 `/scratch/stefan/7786230/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450372/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450372 none CC(C)CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 30, 74, 74, 74, 74, 74, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 74, 1, 2, 2, 2, 11, 11, 11, 11] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 167 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: REAL300024450372 none CC(C)CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 106, 106, 106, 74, 74, 74, 74, 74, 69, 26, 69, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 74, 74, 74, 74, 74, 74, 74, 26, 26, 1, 74, 74, 74, 74, 201, 201, 201, 201] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 634 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450372 none CC(C)CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 20, 20, 61, 117, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 11, 11, 11, 11, 11, 11, 11, 61, 61, 201, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 471 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450372 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450372 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450372/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450372 Building REAL300024450373 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450373' /scratch/stefan/7786230/working/building/REAL300024450373 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450373 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450373/0 /scratch/stefan/7786230/working/building/REAL300024450373 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/234 `/scratch/stefan/7786230/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450373/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450373 none COCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 142, 137, 141, 78, 137, 78, 78, 74, 74, 74, 74, 74, 69, 26, 69, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 142, 142, 142, 142, 137, 137, 137, 137, 78, 74, 74, 74, 74, 74, 74, 74, 26, 26, 1, 74, 74, 74, 74] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 884 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450373 none COCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 21, 9, 7, 8, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 74, 74, 74, 74, 74, 1, 1, 33, 33, 33, 21, 21, 9, 9, 9, 9, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 74, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 236 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450373 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450373 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450373/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450373 Building REAL300024450374 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450374' /scratch/stefan/7786230/working/building/REAL300024450374 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450374 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450374/0 /scratch/stefan/7786230/working/building/REAL300024450374 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/235 `/scratch/stefan/7786230/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450374/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450374 none CC1C(NC(=O)CC2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 41, 41, 101, 131, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 23, 5, 5, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 101, 101, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 577 number of broken/clashed sets: 31 ./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: REAL300024450374 none CC1C(NC(=O)CC2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 105, 105, 105, 197, 201, 201, 201, 201, 201, 99, 99, 99, 83, 27, 83, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 105, 197, 197, 201, 201, 201, 201, 201, 201, 99, 99, 99, 99, 99, 99, 27, 27, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 740 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450374 none CC1C(NC(=O)CC2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 3, 3, 12, 24, 99, 99, 99, 99, 99, 2, 2, 2, 1, 1, 3, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 12, 12, 99] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450374 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450374 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450374/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450374 Building REAL300024450375 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450375' /scratch/stefan/7786230/working/building/REAL300024450375 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450375 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450375/0 /scratch/stefan/7786230/working/building/REAL300024450375 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/236 `/scratch/stefan/7786230/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@]23C[C@H]2COC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450375/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450375 none CC1C(NC(=O)[C@]23C[C@H]2COC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 50, 99, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 50, 50, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 423 number of broken/clashed sets: 24 ./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: REAL300024450375 none CC1C(NC(=O)[C@]23C[C@H]2COC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 81, 81, 81, 201, 201, 201, 201, 201, 201, 79, 79, 79, 78, 42, 78, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 81, 201, 201, 201, 201, 201, 201, 79, 79, 79, 79, 79, 79, 42, 42, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 430 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450375 none CC1C(NC(=O)[C@]23C[C@H]2COC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 12, 32, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 79] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450375 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450375 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450375/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450375 Building REAL300024450376 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450376' /scratch/stefan/7786230/working/building/REAL300024450376 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300024450376 as failed and skipping /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `/scratch/stefan/7786230/failed' `/scratch/stefan/7786230/working/building/REAL300024450376' -> `/scratch/stefan/7786230/failed/REAL300024450376' Building REAL300024450377 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450377' /scratch/stefan/7786230/working/building/REAL300024450377 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450377 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450377/0 /scratch/stefan/7786230/working/building/REAL300024450377 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/237 `/scratch/stefan/7786230/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450377/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450377 none CC1C(NC(=O)C2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 6, 6, 1, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 47, 95, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 6, 2, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 47, 47, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 36] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 430 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: REAL300024450377 none CC1C(NC(=O)C2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 117, 117, 117, 201, 201, 201, 116, 116, 116, 114, 54, 114, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 117, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 116, 54, 54, 1] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 695 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450377 none CC1C(NC(=O)C2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 32, 116, 116, 116, 116, 116, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 116] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 27, 28, 42] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 207 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450377 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450377 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450377/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450377 Building REAL300024450378 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450378' /scratch/stefan/7786230/working/building/REAL300024450378 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450378 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450378/0 /scratch/stefan/7786230/working/building/REAL300024450378 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/238 `/scratch/stefan/7786230/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450378/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450378 none CC1CCCC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 28, 117, 117, 117, 117, 117, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 117, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 232 number of broken/clashed sets: 28 ./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: REAL300024450378 none CC1CCCC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 127, 127, 127, 117, 117, 117, 117, 117, 103, 31, 103, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 117, 117, 117, 117, 117, 117, 117, 31, 31, 1, 117, 117, 117, 117] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 747 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450378 none CC1CCCC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 10, 10, 10, 15, 15, 15, 15, 15, 24, 24, 76, 126, 201, 201, 201, 201, 201, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 15, 15, 15, 15, 15, 15, 15, 76, 76, 201, 15, 15, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 512 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450378 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450378 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450378/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450378 Building REAL300024450379 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450379' /scratch/stefan/7786230/working/building/REAL300024450379 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450379 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450379/0 /scratch/stefan/7786230/working/building/REAL300024450379 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/239 `/scratch/stefan/7786230/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450379/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450379 none CCC(=O)NC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 165, 165, 165, 147, 79, 147, 79, 79, 73, 73, 73, 73, 73, 73, 27, 73, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 165, 147, 147, 147, 147, 79, 73, 73, 73, 73, 73, 73, 73, 27, 27, 1, 73, 73, 73, 73] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 835 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450379 none CCC(=O)NC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 16, 16, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 16, 73, 73, 73, 73, 73, 1, 1, 46, 46, 46, 46, 46, 16, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 73, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450379 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450379 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450379/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450379 Building REAL300024450380 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450380' /scratch/stefan/7786230/working/building/REAL300024450380 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450380 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450380/0 /scratch/stefan/7786230/working/building/REAL300024450380 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/240 `/scratch/stefan/7786230/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(=O)N(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450380/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450380 none CC1C(NC(=O)C2CC(=O)N(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 33, 33, 81, 107, 167, 167, 167, 167, 167, 23, 23, 23, 23, 23, 9, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 23, 23, 23, 23, 81, 81, 167] 167 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 40, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 481 number of broken/clashed sets: 31 ./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: REAL300024450380 none CC1C(NC(=O)C2CC(=O)N(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 65, 65, 65, 97, 97, 97, 167, 167, 167, 167, 167, 167, 65, 65, 65, 62, 38, 62, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 97, 167, 167, 167, 167, 167, 167, 167, 167, 65, 65, 65, 65, 65, 65, 38, 38, 1] 167 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 541 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450380 none CC1C(NC(=O)C2CC(=O)N(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 12, 21, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 12, 12, 65] 167 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450380 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450380 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450380/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450380 Building REAL300024450381 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450381' /scratch/stefan/7786230/working/building/REAL300024450381 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450381 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450381/0 /scratch/stefan/7786230/working/building/REAL300024450381 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/241 `/scratch/stefan/7786230/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450381/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450381 none CNC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 79, 79, 79, 62, 62, 62, 62, 62, 62, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 197, 197, 79, 62, 62, 62, 62, 62, 62, 62, 27, 27, 1, 62, 62, 62, 62] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 764 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450381 none CNC(=O)NCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 30, 30, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 62, 62, 62, 62, 62, 1, 1, 36, 36, 36, 36, 30, 21, 21, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 62, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450381 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450381 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450381/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450381 Building REAL300024450382 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450382' /scratch/stefan/7786230/working/building/REAL300024450382 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450382 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450382/0 /scratch/stefan/7786230/working/building/REAL300024450382 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/242 `/scratch/stefan/7786230/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450382/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450382 none CC1C(NC(=O)[C@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 63, 117, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 63, 63, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 480 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: REAL300024450382 none CC1C(NC(=O)[C@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [127, 127, 127, 127, 151, 151, 151, 201, 201, 201, 201, 201, 127, 127, 127, 123, 51, 123, 12, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 151, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 51, 51, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 668 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450382 none CC1C(NC(=O)[C@H]2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 12, 35, 127, 127, 127, 127, 127, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 127] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450382 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450382 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450382/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450382 Building REAL300024450383 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450383' /scratch/stefan/7786230/working/building/REAL300024450383 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450383 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450383/0 /scratch/stefan/7786230/working/building/REAL300024450383 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/243 `/scratch/stefan/7786230/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450383/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450383 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 196, 83, 83, 83, 75, 75, 75, 75, 75, 68, 26, 68, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 201, 201, 201, 196, 196, 83, 75, 75, 75, 75, 75, 75, 75, 26, 26, 1, 75, 75, 75, 75, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 769 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: REAL300024450383 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 8, 23, 23, 23, 30, 30, 30, 30, 30, 43, 43, 94, 135, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 3, 3, 3, 3, 8, 8, 23, 30, 30, 30, 30, 30, 30, 30, 94, 94, 201, 30, 30, 30, 30, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 47, 48, 49, 50, 51, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 563 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450383 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 75, 75, 75, 75, 75, 1, 1, 28, 30, 30, 28, 28, 28, 28, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 75, 1, 2, 2, 2, 30, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 253 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450383 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450383 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450383/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450383 Building REAL300024450384 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450384' /scratch/stefan/7786230/working/building/REAL300024450384 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450384 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450384/0 /scratch/stefan/7786230/working/building/REAL300024450384 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/244 `/scratch/stefan/7786230/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450384/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450384 none CC1=NC=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 40, 40, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 60, 60, 60, 60, 60, 1, 1, 40, 40, 40, 40, 40, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 8 ./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: REAL300024450384 none CC1=NC=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 70, 70, 70, 60, 60, 60, 60, 60, 56, 25, 56, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 159, 159, 70, 60, 60, 60, 60, 60, 60, 60, 25, 25, 1, 60, 60, 60, 60] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 656 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450384 none CC1=NC=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 33, 33, 33, 40, 40, 40, 40, 40, 56, 56, 85, 128, 201, 201, 201, 201, 201, 40, 40, 1, 2, 2, 2, 1, 8, 8, 33, 40, 40, 40, 40, 40, 40, 40, 85, 85, 201, 40, 40, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 551 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450384 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450384 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450384/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450384 Building REAL300024450385 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450385' /scratch/stefan/7786230/working/building/REAL300024450385 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450385 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450385/0 /scratch/stefan/7786230/working/building/REAL300024450385 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/245 `/scratch/stefan/7786230/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2([NH+](C)C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450385/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450385 none CC1C(NC(=O)C2([NH+](C)C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [45, 43, 4, 6, 7, 40, 41, 42, 11, 12, 13, 44] set([0, 1, 2, 3, 5, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 13 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: REAL300024450385 none CC1C(NC(=O)C2([NH+](C)C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 7 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450385 none CC1C(NC(=O)C2([NH+](C)C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 19 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450385 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450385 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450385/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450385 Building REAL300024450386 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450386' /scratch/stefan/7786230/working/building/REAL300024450386 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450386 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450386/0 /scratch/stefan/7786230/working/building/REAL300024450386 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/246 `/scratch/stefan/7786230/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450386/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450386 none CC1C(NC(=O)C(C)(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 93, 93, 93, 176, 176, 176, 201, 201, 64, 64, 64, 63, 46, 63, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 93, 176, 176, 176, 176, 176, 176, 201, 201, 64, 64, 64, 64, 64, 64, 46, 46, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 802 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450386 none CC1C(NC(=O)C(C)(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 16, 16, 16, 24, 24, 1, 1, 1, 1, 1, 3, 3, 11, 20, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 6, 16, 16, 16, 16, 16, 16, 24, 24, 1, 1, 1, 1, 1, 1, 11, 11, 64] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450386 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450386 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450386/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450386 Building REAL300024450387 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450387' /scratch/stefan/7786230/working/building/REAL300024450387 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450387 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450387/0 /scratch/stefan/7786230/working/building/REAL300024450387 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/247 `/scratch/stefan/7786230/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450387/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450387 none CC(C)[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 12 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450387 none CC(C)[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 6, 6, 6, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4] 6 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 36 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450387 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450387 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450387/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450387 Building REAL300024450388 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450388' /scratch/stefan/7786230/working/building/REAL300024450388 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450388 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450388/0 /scratch/stefan/7786230/working/building/REAL300024450388 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/248 `/scratch/stefan/7786230/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1) `REAL300024450388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450388/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450388 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 28, 87, 87, 87, 87, 87, 1, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 87, 1, 2, 2, 2, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 20 ./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: REAL300024450388 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 94, 94, 94, 87, 87, 87, 87, 87, 84, 47, 84, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 94, 87, 87, 87, 87, 87, 87, 87, 47, 47, 1, 87, 87, 87, 87, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 459 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450388 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 13, 13, 13, 13, 13, 19, 19, 51, 95, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 13, 51, 51, 201, 13, 13, 13, 13, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 450 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450388 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450388 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450388/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450388 Building REAL300024450389 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450389' /scratch/stefan/7786230/working/building/REAL300024450389 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450389 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450389/0 /scratch/stefan/7786230/working/building/REAL300024450389 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/249 `/scratch/stefan/7786230/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450389/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450389 none CC1C(NC(=O)CC2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 23, 23, 4, 23, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 43, 43, 79, 128, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 23, 4, 4, 1, 1, 32, 32, 32, 32, 32, 32, 79, 79, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 524 number of broken/clashed sets: 8 ./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: REAL300024450389 none CC1C(NC(=O)CC2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 66, 66, 66, 150, 201, 201, 201, 201, 60, 60, 60, 58, 25, 58, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 66, 150, 150, 201, 201, 60, 60, 60, 60, 60, 60, 25, 25, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 652 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450389 none CC1C(NC(=O)CC2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 20, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 3, 17, 17, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 60] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450389 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450389 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450389/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450389 Building REAL300024450390 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450390' /scratch/stefan/7786230/working/building/REAL300024450390 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450390 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450390/0 /scratch/stefan/7786230/working/building/REAL300024450390 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/250 `/scratch/stefan/7786230/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450390/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450390 none CC1C(NC(=O)C2=CC(=O)NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 46, 99, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 46, 46, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 408 number of broken/clashed sets: 20 ./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: REAL300024450390 none CC1C(NC(=O)C2=CC(=O)NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 84, 84, 84, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 46, 80, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 84, 201, 201, 201, 80, 80, 80, 80, 80, 80, 46, 46, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 441 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450390 none CC1C(NC(=O)C2=CC(=O)NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 11, 31, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 10, 10, 10, 1, 1, 1, 1, 1, 1, 11, 11, 80] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450390 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450390 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450390/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450390 Building REAL300024450391 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450391' /scratch/stefan/7786230/working/building/REAL300024450391 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450391 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450391/0 /scratch/stefan/7786230/working/building/REAL300024450391 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/251 `/scratch/stefan/7786230/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC(=O)N1) `REAL300024450391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450391/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450391 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 26, 83, 83, 83, 83, 83, 1, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 83, 1, 2, 2, 2, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 20 ./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: REAL300024450391 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 102, 102, 102, 83, 83, 83, 83, 83, 80, 43, 80, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 201, 201, 102, 83, 83, 83, 83, 83, 83, 83, 43, 43, 1, 83, 83, 83, 83, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 498 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450391 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 15, 15, 15, 15, 15, 25, 25, 58, 100, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 15, 15, 15, 58, 58, 201, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 45, 46, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 463 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450391 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450391 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450391/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450391 Building REAL300024450392 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450392' /scratch/stefan/7786230/working/building/REAL300024450392 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450392 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450392/0 /scratch/stefan/7786230/working/building/REAL300024450392 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/252 `/scratch/stefan/7786230/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450392/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450392 none CC1C(NC(=O)C2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [4, 37, 6, 7, 40, 10, 11, 39, 38] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) 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.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: REAL300024450392 none CC1C(NC(=O)C2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 7 number of broken/clashed sets: 0 ./output.4.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: REAL300024450392 none CC1C(NC(=O)C2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 9 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450392 none CC1C(NC(=O)C2(C3CC3)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450392 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450392 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450392/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450392 Building REAL300024450393 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450393' /scratch/stefan/7786230/working/building/REAL300024450393 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450393 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450393/0 /scratch/stefan/7786230/working/building/REAL300024450393 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/253 `/scratch/stefan/7786230/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450393/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450393 none COC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 26, 93, 93, 93, 93, 93, 1, 1, 18, 28, 28, 28, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 93, 1, 2, 2, 2, 18, 18] 196 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 33 ./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: REAL300024450393 none COC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [196, 196, 196, 196, 107, 107, 107, 93, 93, 93, 93, 93, 88, 42, 88, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 196, 196, 196, 196, 196, 196, 196, 196, 107, 93, 93, 93, 93, 93, 93, 93, 42, 42, 1, 93, 93, 93, 93, 196, 196] 196 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 639 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450393 none COC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 18, 18, 25, 25, 63, 99, 196, 196, 196, 196, 196, 18, 18, 1, 3, 3, 3, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 63, 63, 196, 18, 18, 18, 18, 1, 1] 196 rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 49, 25, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 454 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450393 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450393 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450393/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450393 Building REAL300024450394 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450394' /scratch/stefan/7786230/working/building/REAL300024450394 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450394 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450394/0 /scratch/stefan/7786230/working/building/REAL300024450394 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/254 `/scratch/stefan/7786230/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450394/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450394 none CC1C(NC(=O)[C@H]2CCCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 20, 20, 61, 86, 142, 142, 142, 142, 142, 15, 15, 15, 15, 15, 11, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 61, 61, 142] 142 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 368 number of broken/clashed sets: 25 ./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: REAL300024450394 none CC1C(NC(=O)[C@H]2CCCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 80, 80, 80, 142, 142, 142, 142, 142, 142, 142, 67, 67, 67, 62, 37, 62, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 80, 142, 142, 142, 142, 142, 142, 142, 67, 67, 67, 67, 67, 67, 37, 37, 1] 142 rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 444 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450394 none CC1C(NC(=O)[C@H]2CCCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 14, 24, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 14, 14, 67] 142 rigid atoms, others: [0, 1, 2, 3, 32, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 46, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450394 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450394 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450394/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450394 Building REAL300024450395 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450395' /scratch/stefan/7786230/working/building/REAL300024450395 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450395 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450395/0 /scratch/stefan/7786230/working/building/REAL300024450395 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/255 `/scratch/stefan/7786230/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450395/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450395 none CC1C(NC(=O)CCC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 31, 31, 12, 31, 6, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 43, 43, 90, 130, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 31, 12, 12, 6, 6, 1, 1, 1, 38, 38, 38, 38, 38, 38, 90, 90, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 565 number of broken/clashed sets: 41 ./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: REAL300024450395 none CC1C(NC(=O)CCC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 87, 87, 87, 178, 192, 201, 201, 201, 201, 58, 58, 58, 56, 33, 56, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 87, 178, 178, 192, 192, 201, 201, 201, 58, 58, 58, 58, 58, 58, 33, 33, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 779 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450395 none CC1C(NC(=O)CCC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 16, 21, 38, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 11, 19, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 5, 16, 16, 21, 21, 38, 38, 38, 1, 1, 1, 1, 1, 1, 11, 11, 58] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450395 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450395/1 /scratch/stefan/7786230/working/building/REAL300024450395 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/256 `/scratch/stefan/7786230/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450395.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450395/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450395 none CC1C(NC(=O)CCC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 14, 14, 7, 14, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 21, 22, 24, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 14, 7, 7, 4, 4, 1, 1, 1, 15, 15, 15, 15, 15, 15, 22, 22, 29] 29 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 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: REAL300024450395 none CC1C(NC(=O)CCC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 17, 17, 17, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 15, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 17, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 15, 15, 1] 29 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 112 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450395 none CC1C(NC(=O)CCC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 13, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 5, 8, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 3, 11, 11, 13, 13, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 5, 16] 29 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450395 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450395 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450395/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450395/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450395 Building REAL300024450396 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450396' /scratch/stefan/7786230/working/building/REAL300024450396 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450396 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450396/0 /scratch/stefan/7786230/working/building/REAL300024450396 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/257 `/scratch/stefan/7786230/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450396/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450396 none CC1C(NC(=O)C[N@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 19, 19, 6, 19, 3, 1, 3, 3, 1, 1, 1, 1, 39, 39, 39, 39, 39, 56, 56, 106, 140, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 19, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 106, 106, 201] 201 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 44, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 585 number of broken/clashed sets: 24 ./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: REAL300024450396 none CC1C(NC(=O)C[N@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 96, 96, 145, 145, 145, 200, 201, 201, 201, 201, 201, 201, 96, 96, 96, 83, 30, 83, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 145, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 30, 30, 1] 201 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 737 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450396 none CC1C(NC(=O)C[N@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 21, 28, 28, 28, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 12, 21, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 6, 21, 21, 28, 28, 28, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 12, 12, 96] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 313 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450396 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450396/1 /scratch/stefan/7786230/working/building/REAL300024450396 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/258 `/scratch/stefan/7786230/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450396.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450396/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450396 none CC1C(NC(=O)C[N@@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 17, 17, 6, 17, 2, 1, 2, 2, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 98, 134, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 17, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 98, 98, 201] 201 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 44, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 567 number of broken/clashed sets: 23 ./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: REAL300024450396 none CC1C(NC(=O)C[N@@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [94, 94, 94, 94, 149, 149, 149, 199, 201, 201, 201, 201, 201, 201, 94, 94, 94, 83, 29, 83, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 149, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 94, 94, 94, 29, 29, 1] 201 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 742 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450396 none CC1C(NC(=O)C[N@@H+](C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 25, 25, 25, 34, 34, 34, 1, 1, 1, 1, 1, 3, 3, 12, 20, 94, 94, 94, 94, 94, 2, 2, 2, 1, 1, 6, 19, 19, 25, 25, 25, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 12, 12, 94] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 291 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450396 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450396 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450396/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450396/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450396 Building REAL300024450397 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450397' /scratch/stefan/7786230/working/building/REAL300024450397 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450397 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450397/0 /scratch/stefan/7786230/working/building/REAL300024450397 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/259 `/scratch/stefan/7786230/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450397/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450397 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 28, 45, 86, 86, 86, 86, 86, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 86] 86 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 18 ./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: REAL300024450397 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 86, 86, 86, 86, 86, 86, 86, 86, 86, 82, 82, 82, 79, 41, 79, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 86, 86, 86, 86, 82, 82, 82, 82, 82, 82, 41, 41, 1] 86 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 288 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450397 none CC1C(NC(=O)C2=CC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 3, 3, 15, 32, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 15, 82] 86 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450397 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450397 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450397/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450397 Building REAL300024450398 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450398' /scratch/stefan/7786230/working/building/REAL300024450398 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450398 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450398/0 /scratch/stefan/7786230/working/building/REAL300024450398 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/260 `/scratch/stefan/7786230/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450398/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450398 none C=CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 127, 124, 117, 57, 57, 57, 47, 47, 47, 47, 47, 47, 24, 47, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 127, 127, 117, 117, 57, 47, 47, 47, 47, 47, 47, 47, 24, 24, 1, 47, 47, 47, 47] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 875 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450398 none C=CCCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 32, 20, 15, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 47, 47, 47, 47, 47, 1, 1, 37, 37, 37, 32, 32, 20, 20, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 47, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450398 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450398 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450398/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450398 Building REAL300024450399 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450399' /scratch/stefan/7786230/working/building/REAL300024450399 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450399 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450399/0 /scratch/stefan/7786230/working/building/REAL300024450399 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/261 `/scratch/stefan/7786230/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450399/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450399 none C=CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 169, 110, 169, 110, 110, 96, 96, 96, 96, 96, 89, 31, 89, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 169, 169, 169, 169, 110, 96, 96, 96, 96, 96, 96, 96, 31, 31, 1, 96, 96, 96, 96] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 807 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450399 none C=CCOC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 9, 6, 3, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 96, 96, 96, 96, 96, 1, 1, 39, 39, 39, 22, 22, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 96, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 290 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450399 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450399 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450399/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450399 Building REAL300024450400 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450400' /scratch/stefan/7786230/working/building/REAL300024450400 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450400 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450400/0 /scratch/stefan/7786230/working/building/REAL300024450400 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/262 `/scratch/stefan/7786230/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450400/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450400 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 5, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 32, 107, 107, 107, 107, 107, 1, 1, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 107, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 212 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: REAL300024450400 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 184, 201, 201, 114, 114, 114, 107, 107, 107, 107, 107, 100, 49, 100, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 114, 107, 107, 107, 107, 107, 107, 107, 49, 49, 1, 107, 107, 107, 107] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450400 none CC1=CN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 14, 14, 14, 14, 14, 23, 23, 64, 117, 201, 201, 201, 201, 201, 14, 14, 2, 2, 2, 1, 1, 1, 10, 14, 14, 14, 14, 14, 14, 14, 64, 64, 201, 14, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 475 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450400 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450400 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450400/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450400 Building REAL300024450401 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450401' /scratch/stefan/7786230/working/building/REAL300024450401 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450401 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450401/0 /scratch/stefan/7786230/working/building/REAL300024450401 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/263 `/scratch/stefan/7786230/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450401/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450401 none CC1C(NC(=O)C2CCC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 23, 23, 64, 115, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 11, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 64, 64, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 45]) total number of confs: 472 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: REAL300024450401 none CC1C(NC(=O)C2CCC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 105, 105, 105, 201, 201, 201, 201, 201, 99, 99, 99, 97, 52, 97, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 105, 201, 201, 201, 201, 201, 99, 99, 99, 99, 99, 99, 52, 52, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 625 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450401 none CC1C(NC(=O)C2CCC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 31, 99, 99, 99, 99, 99, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 99] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450401 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450401 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450401/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450401 Building REAL300024450402 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450402' /scratch/stefan/7786230/working/building/REAL300024450402 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450402 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450402/0 /scratch/stefan/7786230/working/building/REAL300024450402 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/264 `/scratch/stefan/7786230/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NSC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450402/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450402 none CC1C(NC(=O)C2=NSC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 44, 101, 197, 197, 197, 197, 197, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 44, 44, 197] 197 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 406 number of broken/clashed sets: 27 ./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: REAL300024450402 none CC1C(NC(=O)C2=NSC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [191, 191, 191, 191, 197, 197, 197, 197, 197, 197, 197, 191, 191, 191, 184, 71, 184, 13, 1, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 197, 197, 197, 191, 191, 191, 191, 191, 191, 71, 71, 1] 197 rigid atoms, others: [41, 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]) total number of confs: 586 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450402 none CC1C(NC(=O)C2=NSC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 17, 56, 191, 191, 191, 191, 191, 2, 2, 2, 1, 1, 4, 8, 8, 1, 1, 1, 1, 1, 1, 17, 17, 191] 197 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450402 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450402 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450402/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450402 Building REAL300024450403 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450403' /scratch/stefan/7786230/working/building/REAL300024450403 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450403 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450403/0 /scratch/stefan/7786230/working/building/REAL300024450403 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/265 `/scratch/stefan/7786230/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1) `REAL300024450403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450403/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450403 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 124, 124, 124, 113, 113, 113, 113, 113, 97, 28, 97, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 124, 113, 113, 113, 113, 113, 113, 113, 28, 28, 1, 113, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 739 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: REAL300024450403 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 16, 16, 16, 20, 20, 20, 20, 20, 30, 30, 86, 136, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 1, 4, 4, 4, 4, 16, 20, 20, 20, 20, 20, 20, 20, 86, 86, 201, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 51, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 528 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450403 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 113, 113, 113, 113, 113, 1, 1, 13, 20, 20, 20, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 113, 1, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450403 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450403 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450403/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450403 Building REAL300024450404 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450404' /scratch/stefan/7786230/working/building/REAL300024450404 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450404 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450404/0 /scratch/stefan/7786230/working/building/REAL300024450404 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/266 `/scratch/stefan/7786230/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450404/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450404 none CC1C(NC(=O)CC2C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 44, 44, 80, 123, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 80, 80, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 528 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: REAL300024450404 none CC1C(NC(=O)CC2C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 83, 83, 83, 194, 201, 201, 201, 201, 201, 69, 69, 69, 67, 29, 67, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 83, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 29, 29, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 765 number of broken/clashed sets: 4 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450404 none CC1C(NC(=O)CC2C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 10, 17, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 4, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 10, 10, 69] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450404 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450404 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450404/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450404 Building REAL300024450405 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450405' /scratch/stefan/7786230/working/building/REAL300024450405 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450405 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450405/0 /scratch/stefan/7786230/working/building/REAL300024450405 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/267 `/scratch/stefan/7786230/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450405/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450405 none CCOCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 24, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 62, 62, 62, 62, 62, 1, 1, 11, 11, 38, 38, 38, 38, 38, 24, 24, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 62, 1, 2, 2, 2, 11, 11, 11, 11] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 225 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: REAL300024450405 none CCOCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 176, 79, 79, 79, 62, 62, 62, 62, 62, 61, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 176, 176, 201, 201, 201, 201, 201, 201, 201, 79, 62, 62, 62, 62, 62, 62, 62, 27, 27, 1, 62, 62, 62, 62, 176, 176, 176, 176] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 667 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450405 none CCOCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 16, 8, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 19, 19, 42, 79, 176, 176, 176, 176, 176, 11, 11, 1, 1, 19, 19, 19, 19, 19, 8, 8, 6, 11, 11, 11, 11, 11, 11, 11, 42, 42, 176, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 446 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450405 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450405 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450405/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450405 Building REAL300024450406 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450406' /scratch/stefan/7786230/working/building/REAL300024450406 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450406 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450406/0 /scratch/stefan/7786230/working/building/REAL300024450406 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/268 `/scratch/stefan/7786230/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3C=CC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450406/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450406 none CC1C(NC(=O)C2CC3C=CC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 15, 15, 57, 92, 162, 162, 162, 162, 162, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 57, 57, 162] 162 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 387 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: REAL300024450406 none CC1C(NC(=O)C2CC3C=CC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 110, 110, 110, 162, 162, 162, 162, 162, 162, 98, 98, 98, 92, 43, 92, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 110, 162, 162, 162, 162, 162, 162, 162, 98, 98, 98, 98, 98, 98, 43, 43, 1] 162 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 554 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450406 none CC1C(NC(=O)C2CC3C=CC2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 14, 29, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 14, 14, 98] 162 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450406 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450406 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450406/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450406 Building REAL300024450407 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450407' /scratch/stefan/7786230/working/building/REAL300024450407 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450407 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450407/0 /scratch/stefan/7786230/working/building/REAL300024450407 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/269 `/scratch/stefan/7786230/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450407/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450407 none COC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 14, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 27, 120, 120, 120, 120, 120, 1, 1, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 120, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 233 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: REAL300024450407 none COC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 132, 132, 132, 120, 120, 120, 120, 120, 112, 31, 112, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 120, 120, 120, 120, 120, 120, 120, 31, 31, 1, 120, 120, 120, 120] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 592 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450407 none COC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 14, 14, 14, 14, 22, 22, 62, 102, 201, 201, 201, 201, 201, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 14, 14, 14, 14, 14, 62, 62, 201, 14, 14, 14, 14] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 467 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450407 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450407 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450407/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450407 Building REAL300024450408 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450408' /scratch/stefan/7786230/working/building/REAL300024450408 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450408 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450408/0 /scratch/stefan/7786230/working/building/REAL300024450408 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/270 `/scratch/stefan/7786230/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CO1) `REAL300024450408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450408/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450408 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 22, 69, 69, 69, 69, 69, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 69, 1, 2, 2, 2, 25, 25] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 38 ./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: REAL300024450408 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 99, 99, 99, 69, 69, 69, 69, 69, 63, 36, 63, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 69, 69, 69, 69, 69, 69, 69, 36, 36, 1, 69, 69, 69, 69, 201, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49]) total number of confs: 640 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450408 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 25, 25, 25, 25, 25, 37, 37, 95, 128, 201, 201, 201, 201, 201, 25, 25, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 95, 95, 201, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 48, 49, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450408 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450408 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450408/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450408 Building REAL300024450409 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450409' /scratch/stefan/7786230/working/building/REAL300024450409 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450409 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450409/0 /scratch/stefan/7786230/working/building/REAL300024450409 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/271 `/scratch/stefan/7786230/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450409/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450409 none CC1C(NC(=O)C2CCCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 23, 23, 72, 120, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 72, 72, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 496 number of broken/clashed sets: 41 ./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: REAL300024450409 none CC1C(NC(=O)C2CCCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 90, 90, 90, 201, 201, 201, 201, 201, 201, 80, 80, 80, 75, 40, 75, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 80, 40, 40, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 619 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450409 none CC1C(NC(=O)C2CCCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 12, 26, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 12, 12, 80] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450409 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450409 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450409/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450409 Building REAL300024450410 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450410' /scratch/stefan/7786230/working/building/REAL300024450410 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450410 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450410/0 /scratch/stefan/7786230/working/building/REAL300024450410 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/272 `/scratch/stefan/7786230/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450410/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450410 none CC1C(NC(=O)CC2CCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 26, 26, 6, 26, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 55, 55, 101, 136, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 101, 101, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 574 number of broken/clashed sets: 14 ./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: REAL300024450410 none CC1C(NC(=O)CC2CCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 74, 74, 74, 189, 201, 201, 201, 201, 201, 67, 67, 67, 59, 25, 59, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 74, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 25, 25, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 763 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450410 none CC1C(NC(=O)CC2CCC3CC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 10, 16, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 3, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 10, 10, 67] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450410 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450410 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450410/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450410 Building REAL300024450411 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450411' /scratch/stefan/7786230/working/building/REAL300024450411 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450411 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450411/0 /scratch/stefan/7786230/working/building/REAL300024450411 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/273 `/scratch/stefan/7786230/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450411/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450411 none CC1C(NC(=O)C2CCC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 32, 32, 83, 119, 196, 196, 196, 196, 196, 20, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 83, 83, 196] 196 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 537 number of broken/clashed sets: 34 ./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: REAL300024450411 none CC1C(NC(=O)C2CCC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 96, 96, 96, 196, 196, 196, 196, 196, 196, 66, 66, 66, 63, 40, 63, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 96, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 66, 66, 66, 66, 66, 66, 40, 40, 1] 196 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 651 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450411 none CC1C(NC(=O)C2CCC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 3, 13, 21, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 13, 13, 66] 196 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450411 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450411 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450411/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450411 Building REAL300024450412 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450412' /scratch/stefan/7786230/working/building/REAL300024450412 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450412 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450412/0 /scratch/stefan/7786230/working/building/REAL300024450412 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/274 `/scratch/stefan/7786230/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450412/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450412 none CCC(C)C(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 174, 201, 91, 174, 174, 91, 91, 67, 67, 67, 67, 67, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 91, 67, 67, 67, 67, 67, 67, 67, 37, 37, 1, 67, 67, 67, 67] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 854 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450412 none CCC(C)C(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 16, 11, 16, 3, 11, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 67, 67, 67, 67, 67, 1, 1, 22, 22, 22, 22, 22, 16, 16, 16, 16, 11, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 67, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450412 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450412 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450412/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450412 Building REAL300024450413 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450413' /scratch/stefan/7786230/working/building/REAL300024450413 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450413 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450413/0 /scratch/stefan/7786230/working/building/REAL300024450413 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/275 `/scratch/stefan/7786230/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450413/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450413 none COC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 81, 81, 81, 81, 81, 1, 1, 12, 26, 26, 26, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 81, 1, 2, 2, 2, 12, 12] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 196 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: REAL300024450413 none COC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 87, 87, 81, 81, 81, 81, 81, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 81, 81, 81, 81, 81, 81, 81, 39, 39, 1, 81, 81, 81, 81, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 604 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450413 none COC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 12, 12, 12, 12, 12, 19, 19, 65, 102, 201, 201, 201, 201, 201, 12, 12, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 12, 12, 12, 12, 65, 65, 201, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 52, 26, 51, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 481 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450413 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450413 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450413/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450413 Building REAL300024450414 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450414' /scratch/stefan/7786230/working/building/REAL300024450414 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450414 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450414/0 /scratch/stefan/7786230/working/building/REAL300024450414 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/276 `/scratch/stefan/7786230/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2OCCO[C@H]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450414/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450414 none CC1C(NC(=O)[C@H]2OCCO[C@H]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 55, 82, 144, 144, 144, 144, 144, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 55, 55, 144] 144 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 363 number of broken/clashed sets: 34 ./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: REAL300024450414 none CC1C(NC(=O)[C@H]2OCCO[C@H]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 88, 88, 88, 115, 115, 115, 144, 144, 144, 144, 144, 144, 144, 144, 88, 88, 88, 80, 40, 80, 12, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 115, 144, 144, 144, 144, 144, 144, 144, 88, 88, 88, 88, 88, 88, 40, 40, 1] 144 rigid atoms, others: [50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 497 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450414 none CC1C(NC(=O)[C@H]2OCCO[C@H]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 12, 5, 5, 12, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 16, 29, 88, 88, 88, 88, 88, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 16, 16, 88] 144 rigid atoms, others: [0, 1, 2, 3, 33, 32, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450414 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450414 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450414/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450414 Building REAL300024450415 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450415' /scratch/stefan/7786230/working/building/REAL300024450415 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450415 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450415/0 /scratch/stefan/7786230/working/building/REAL300024450415 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/277 `/scratch/stefan/7786230/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450415/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450415 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 91, 91, 91, 91, 91, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 91, 1, 2, 2, 2] 115 rigid atoms, others: [45, 43, 49, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 188 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: REAL300024450415 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 115, 115, 115, 115, 107, 115, 107, 107, 91, 91, 91, 91, 91, 85, 39, 85, 12, 1, 1, 1, 1, 1, 1, 1, 91, 91, 115, 115, 115, 115, 115, 115, 115, 115, 115, 107, 91, 91, 91, 91, 91, 91, 91, 39, 39, 1, 91, 91, 91, 91] 115 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 386 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450415 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 13, 13, 41, 66, 115, 115, 115, 115, 115, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 41, 41, 115, 9, 9, 9, 9] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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, 50, 51, 52]) total number of confs: 286 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450415 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450415 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450415/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450415 Building REAL300024450416 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450416' /scratch/stefan/7786230/working/building/REAL300024450416 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450416 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450416/0 /scratch/stefan/7786230/working/building/REAL300024450416 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/278 `/scratch/stefan/7786230/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1C1CC1) `REAL300024450416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450416/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450416 none CC1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 28, 121, 121, 121, 121, 121, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 121, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 211 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.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: REAL300024450416 none CC1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 3, 3, 3, 8, 8, 8, 8, 8, 15, 15, 57, 103, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 57, 57, 201, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 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, 20, 21, 22, 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: 460 number of broken/clashed sets: 15 ./output.4.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: REAL300024450416 none CC1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 170, 170, 170, 121, 121, 121, 121, 121, 113, 34, 113, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 121, 121, 121, 121, 121, 121, 121, 34, 34, 1, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 649 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450416 none CC1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 8, 8, 8, 8, 8, 15, 15, 57, 103, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 57, 57, 201, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 47, 23, 24, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 462 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450416 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450416 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450416/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450416 Building REAL300024450417 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450417' /scratch/stefan/7786230/working/building/REAL300024450417 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450417 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450417/0 /scratch/stefan/7786230/working/building/REAL300024450417 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/279 `/scratch/stefan/7786230/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450417/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450417 none CC1C(NC(=O)C2CCCC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 49, 100, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 49, 49, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 434 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: REAL300024450417 none CC1C(NC(=O)C2CCCC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [122, 122, 122, 122, 142, 142, 142, 201, 201, 201, 201, 201, 201, 122, 122, 122, 118, 53, 118, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 122, 53, 53, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 682 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450417 none CC1C(NC(=O)C2CCCC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 11, 36, 122, 122, 122, 122, 122, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 122] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450417 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450417 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450417/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450417 Building REAL300024450418 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450418' /scratch/stefan/7786230/working/building/REAL300024450418 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450418 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450418/0 /scratch/stefan/7786230/working/building/REAL300024450418 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/280 `/scratch/stefan/7786230/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450418/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450418 none CC(C)OCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 168, 189, 67, 67, 67, 57, 57, 57, 57, 57, 55, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 183, 186, 201, 201, 189, 189, 67, 57, 57, 57, 57, 57, 57, 57, 27, 27, 1, 57, 57, 57, 57] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 924 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450418 none CC(C)OCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 22, 31, 17, 13, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 57, 57, 57, 57, 57, 1, 1, 31, 31, 31, 31, 31, 31, 31, 15, 15, 17, 17, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 57, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 248 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450418 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450418 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450418/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450418 Building REAL300024450419 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450419' /scratch/stefan/7786230/working/building/REAL300024450419 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450419 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450419/0 /scratch/stefan/7786230/working/building/REAL300024450419 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/281 `/scratch/stefan/7786230/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450419/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450419 none CC1C(NC(=O)CCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 49, 49, 49, 54, 54, 54, 145, 131, 198, 201, 201, 49, 49, 49, 49, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 54, 145, 145, 163, 163, 181, 183, 201, 201, 49, 49, 49, 49, 49, 49, 31, 31, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 969 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450419 none CC1C(NC(=O)CCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 17, 36, 56, 56, 1, 1, 1, 1, 1, 3, 3, 8, 14, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 3, 13, 13, 22, 22, 32, 31, 56, 56, 1, 1, 1, 1, 1, 1, 8, 8, 49] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 324 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450419 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450419 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450419/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450419 Building REAL300024450420 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450420' /scratch/stefan/7786230/working/building/REAL300024450420 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450420 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450420/0 /scratch/stefan/7786230/working/building/REAL300024450420 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/282 `/scratch/stefan/7786230/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450420/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450420 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 37, 37, 82, 103, 141, 141, 141, 141, 141, 27, 27, 27, 27, 27, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 82, 82, 141] 141 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 44, 43, 45, 36, 38, 42] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 433 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: REAL300024450420 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 52, 52, 52, 81, 81, 81, 141, 141, 141, 141, 141, 141, 141, 52, 52, 52, 52, 32, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 81, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 52, 52, 52, 52, 52, 52, 32, 32, 1] 141 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 469 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450420 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 9, 17, 52, 52, 52, 52, 52, 2, 2, 2, 1, 1, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 9, 9, 52] 141 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450420 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450420 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450420/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450420 Building REAL300024450421 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450421' /scratch/stefan/7786230/working/building/REAL300024450421 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450421 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450421/0 /scratch/stefan/7786230/working/building/REAL300024450421 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/283 `/scratch/stefan/7786230/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450421/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450421 none CCC(CC)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 141, 141, 143, 201, 67, 141, 67, 67, 63, 63, 63, 63, 63, 59, 26, 59, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 199, 201, 143, 201, 201, 201, 201, 201, 141, 141, 141, 141, 67, 63, 63, 63, 63, 63, 63, 63, 26, 26, 1, 63, 63, 63, 63] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 1270 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450421 none CCC(CC)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 11, 10, 12, 16, 3, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 63, 63, 63, 63, 63, 1, 1, 16, 16, 16, 15, 16, 12, 16, 16, 16, 16, 16, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 212 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450421 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450421 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450421/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450421 Building REAL300024450422 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450422' /scratch/stefan/7786230/working/building/REAL300024450422 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450422 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450422/0 /scratch/stefan/7786230/working/building/REAL300024450422 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/284 `/scratch/stefan/7786230/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(F)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450422/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450422 none CC1C(NC(=O)C2(F)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 58, 109, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 58, 58, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 458 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: REAL300024450422 none CC1C(NC(=O)C2(F)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 107, 107, 107, 117, 117, 117, 201, 201, 201, 201, 201, 107, 107, 107, 106, 47, 106, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 117, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 107, 107, 107, 47, 47, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 634 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450422 none CC1C(NC(=O)C2(F)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 12, 33, 107, 107, 107, 107, 107, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 107] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450422 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450422 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450422/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450422 Building REAL300024450423 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450423' /scratch/stefan/7786230/working/building/REAL300024450423 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450423 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450423/0 /scratch/stefan/7786230/working/building/REAL300024450423 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/285 `/scratch/stefan/7786230/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450423/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450423 none CC1C(NC(=O)C2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 57, 113, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 57, 57, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 452 number of broken/clashed sets: 38 ./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: REAL300024450423 none CC1C(NC(=O)C2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [135, 135, 135, 135, 171, 171, 171, 201, 201, 201, 201, 201, 135, 135, 135, 134, 62, 134, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 171, 201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 135, 62, 62, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 608 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450423 none CC1C(NC(=O)C2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 15, 43, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 15, 15, 135] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450423 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450423 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450423/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450423 Building REAL300024450424 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450424' /scratch/stefan/7786230/working/building/REAL300024450424 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450424 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450424/0 /scratch/stefan/7786230/working/building/REAL300024450424 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/286 `/scratch/stefan/7786230/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C) `REAL300024450424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450424/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450424 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 5 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450424 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 4 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 21 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450424 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450424 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450424/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450424 Building REAL300024450425 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450425' /scratch/stefan/7786230/working/building/REAL300024450425 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450425 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450425/0 /scratch/stefan/7786230/working/building/REAL300024450425 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/287 `/scratch/stefan/7786230/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CCC(CC2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450425/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450425 none CC1C(NC(=O)C23CCC(CC2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 19, 19, 52, 91, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 52, 52, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 431 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: REAL300024450425 none CC1C(NC(=O)C23CCC(CC2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 67, 67, 67, 201, 201, 201, 201, 201, 201, 66, 66, 66, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 37, 37, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 399 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450425 none CC1C(NC(=O)C23CCC(CC2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 11, 24, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 11, 11, 66] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450425 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450425 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450425/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450425 Building REAL300024450426 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450426' /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450426 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450426/0 /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/288 `/scratch/stefan/7786230/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450426/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4] 4 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 15 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: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 5 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4] 4 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450426/1 /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/289 `/scratch/stefan/7786230/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450426.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450426/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 16, 21, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 16, 16, 26] 26 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 8 ./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: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 16, 21, 10, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 16, 16, 1] 26 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 78 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 8, 13, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 21] 26 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450426/2 /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/290 `/scratch/stefan/7786230/working/3D/290' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450426.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450426/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 28, 51, 86, 86, 86, 86, 86, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 28, 28, 86] 86 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 208 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: REAL300024450426 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 86, 86, 86, 86, 86, 86, 71, 71, 71, 68, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 71, 71, 71, 71, 71, 71, 36, 36, 1] 86 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 294 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450426 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 16, 33, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 16, 16, 71] 86 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 13, 14, 45, 16, 49, 50, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450426 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450426 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450426/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450426/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450426/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450426 Building REAL300024450427 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450427' /scratch/stefan/7786230/working/building/REAL300024450427 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450427 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450427/0 /scratch/stefan/7786230/working/building/REAL300024450427 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/291 `/scratch/stefan/7786230/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450427/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450427 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 36, 36, 86, 132, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 17, 7, 7, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 86, 86, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 571 number of broken/clashed sets: 54 ./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: REAL300024450427 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 33, 33, 53, 53, 53, 122, 201, 201, 201, 201, 201, 33, 33, 33, 33, 22, 33, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 53, 122, 122, 201, 201, 201, 201, 33, 33, 33, 33, 33, 33, 22, 22, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 649 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450427 none CC1C(NC(=O)CC2=CC=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 6, 10, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 4, 12, 12, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 6, 6, 33] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450427 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450427 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450427/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450427 Building REAL300024450428 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450428' /scratch/stefan/7786230/working/building/REAL300024450428 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450428 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450428/0 /scratch/stefan/7786230/working/building/REAL300024450428 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/292 `/scratch/stefan/7786230/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450428/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450428 none CCC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 11, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 112, 112, 112, 112, 112, 1, 1, 11, 22, 22, 22, 22, 22, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 112, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 262 number of broken/clashed sets: 31 ./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: REAL300024450428 none CCC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 159, 159, 137, 137, 137, 112, 112, 112, 112, 112, 103, 42, 103, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 159, 201, 201, 201, 201, 201, 159, 159, 137, 112, 112, 112, 112, 112, 112, 112, 42, 42, 1, 112, 112, 112, 112] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 733 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450428 none CCC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 18, 18, 48, 69, 159, 159, 159, 159, 159, 11, 11, 1, 6, 6, 6, 5, 5, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 48, 48, 159, 11, 11, 11, 11] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 367 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450428 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450428 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450428/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450428 Building REAL300024450429 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450429' /scratch/stefan/7786230/working/building/REAL300024450429 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450429 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450429/0 /scratch/stefan/7786230/working/building/REAL300024450429 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/293 `/scratch/stefan/7786230/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450429/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450429 none CC1C(NC(=O)CCC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [63, 63, 63, 63, 73, 73, 73, 172, 173, 201, 201, 201, 63, 63, 63, 61, 36, 61, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 73, 172, 172, 189, 189, 201, 201, 201, 63, 63, 63, 63, 63, 63, 36, 36, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 934 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450429 none CC1C(NC(=O)CCC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 19, 43, 43, 43, 1, 1, 1, 1, 1, 3, 3, 10, 17, 63, 63, 63, 63, 63, 2, 2, 2, 1, 1, 4, 15, 15, 23, 23, 43, 43, 43, 1, 1, 1, 1, 1, 1, 10, 10, 63] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450429 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450429 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450429/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450429 Building REAL300024450430 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450430' /scratch/stefan/7786230/working/building/REAL300024450430 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450430 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450430/0 /scratch/stefan/7786230/working/building/REAL300024450430 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/294 `/scratch/stefan/7786230/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(=O)NC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450430/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450430 none CC1C(NC(=O)C2CCC(=O)NC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 33, 33, 77, 103, 157, 157, 157, 157, 157, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 77, 77, 157] 157 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 456 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: REAL300024450430 none CC1C(NC(=O)C2CCC(=O)NC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 96, 96, 96, 157, 157, 157, 157, 157, 157, 67, 67, 67, 64, 39, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 96, 157, 157, 157, 157, 157, 157, 157, 157, 67, 67, 67, 67, 67, 67, 39, 39, 1] 157 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 515 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450430 none CC1C(NC(=O)C2CCC(=O)NC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 11, 19, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 67] 157 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450430 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450430 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450430/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450430 Building REAL300024450431 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450431' /scratch/stefan/7786230/working/building/REAL300024450431 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450431 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450431/0 /scratch/stefan/7786230/working/building/REAL300024450431 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/295 `/scratch/stefan/7786230/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450431/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450431 none CCC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 27, 95, 95, 95, 95, 95, 1, 1, 23, 23, 23, 23, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 95, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 40 ./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: REAL300024450431 none CCC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 144, 144, 144, 144, 105, 105, 105, 95, 95, 95, 95, 95, 82, 28, 82, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 201, 201, 144, 144, 105, 95, 95, 95, 95, 95, 95, 95, 28, 28, 1, 95, 95, 95, 95] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 714 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450431 none CCC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 15, 15, 44, 74, 144, 144, 144, 144, 144, 9, 9, 6, 6, 6, 5, 5, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 44, 44, 144, 9, 9, 9, 9] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 353 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450431 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450431 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450431/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450431 Building REAL300024450432 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450432' /scratch/stefan/7786230/working/building/REAL300024450432 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450432 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450432/0 /scratch/stefan/7786230/working/building/REAL300024450432 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/296 `/scratch/stefan/7786230/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450432/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450432 none CC1C(NC(=O)C2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 41, 99, 183, 183, 183, 183, 183, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 41, 41, 183] 183 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 374 number of broken/clashed sets: 35 ./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: REAL300024450432 none CC1C(NC(=O)C2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [178, 178, 178, 178, 183, 183, 183, 183, 183, 183, 183, 178, 178, 178, 166, 65, 166, 13, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 183, 183, 183, 178, 178, 178, 178, 178, 178, 65, 65, 1] 183 rigid atoms, others: [41, 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]) total number of confs: 536 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450432 none CC1C(NC(=O)C2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 18, 68, 178, 178, 178, 178, 178, 2, 2, 2, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 18, 18, 178] 183 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450432 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450432/1 /scratch/stefan/7786230/working/building/REAL300024450432 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/297 `/scratch/stefan/7786230/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450432.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450432/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450432 none CC1C(NC(=O)C2=CN=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 43, 97, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 1, 11, 11, 11, 11, 11, 11, 43, 43, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 409 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: REAL300024450432 none CC1C(NC(=O)C2=CN=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [152, 152, 152, 152, 155, 155, 155, 201, 201, 201, 201, 152, 152, 152, 145, 62, 145, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 155, 201, 201, 152, 152, 152, 152, 152, 152, 62, 62, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 557 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450432 none CC1C(NC(=O)C2=CN=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 15, 50, 152, 152, 152, 152, 152, 2, 2, 2, 1, 1, 4, 11, 11, 1, 1, 1, 1, 1, 1, 15, 15, 152] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 263 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450432 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450432 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450432/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450432/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450432 Building REAL300024450433 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450433' /scratch/stefan/7786230/working/building/REAL300024450433 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450433 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450433/0 /scratch/stefan/7786230/working/building/REAL300024450433 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/298 `/scratch/stefan/7786230/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1) `REAL300024450433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450433/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450433 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 52, 52, 52, 52, 52, 1, 1, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 52, 1, 2, 2, 2, 6, 6] 65 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 10 ./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: REAL300024450433 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 53, 53, 53, 52, 52, 52, 52, 52, 51, 43, 51, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 65, 65, 65, 65, 65, 65, 53, 52, 52, 52, 52, 52, 52, 52, 43, 43, 1, 52, 52, 52, 52, 65, 65] 65 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450433 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 4, 4, 4, 6, 6, 6, 6, 6, 10, 10, 24, 42, 65, 65, 65, 65, 65, 6, 6, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 24, 24, 65, 6, 6, 6, 6, 1, 1] 65 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450433 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450433 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450433/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450433 Building REAL300024450434 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450434' /scratch/stefan/7786230/working/building/REAL300024450434 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450434 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450434/0 /scratch/stefan/7786230/working/building/REAL300024450434 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/299 `/scratch/stefan/7786230/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450434/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450434 none CC1C(NC(=O)CC2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 24, 24, 5, 24, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 47, 47, 98, 136, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 24, 5, 5, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 98, 98, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 575 number of broken/clashed sets: 23 ./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: REAL300024450434 none CC1C(NC(=O)CC2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 78, 78, 78, 171, 201, 201, 201, 201, 201, 72, 72, 72, 66, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 78, 171, 171, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 72, 72, 27, 27, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 753 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450434 none CC1C(NC(=O)CC2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 11, 18, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 3, 14, 14, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 11, 11, 72] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450434 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450434 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450434/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450434 Building REAL300024450435 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450435' /scratch/stefan/7786230/working/building/REAL300024450435 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450435 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450435/0 /scratch/stefan/7786230/working/building/REAL300024450435 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/300 `/scratch/stefan/7786230/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450435/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450435 none CNC(=O)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 11, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 26, 26, 26, 26, 26, 1, 1, 11, 11, 19, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 1, 2, 2, 2, 11, 11, 11, 11] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 10 ./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: REAL300024450435 none CNC(=O)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 57, 68, 30, 30, 30, 26, 26, 26, 26, 26, 26, 20, 26, 13, 1, 1, 1, 1, 1, 1, 1, 26, 26, 57, 57, 68, 68, 68, 68, 30, 26, 26, 26, 26, 26, 26, 26, 20, 20, 1, 26, 26, 26, 26, 57, 57, 57, 57] 68 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450435 none CNC(=O)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 14, 14, 26, 35, 57, 57, 57, 57, 57, 11, 11, 1, 1, 5, 5, 5, 5, 7, 11, 11, 11, 11, 11, 11, 11, 26, 26, 57, 11, 11, 11, 11, 1, 1, 1, 1] 68 rigid atoms, others: [2, 4, 5, 46, 47, 48, 49, 25, 26] set([0, 1, 3, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 169 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450435 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450435 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450435/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450435 Building REAL300024450436 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450436' /scratch/stefan/7786230/working/building/REAL300024450436 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450436 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450436/0 /scratch/stefan/7786230/working/building/REAL300024450436 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/301 `/scratch/stefan/7786230/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450436/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450436 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 24, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 63, 63, 63, 63, 63, 1, 1, 12, 12, 32, 32, 32, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 1, 2, 2, 2, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 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: REAL300024450436 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 172, 68, 68, 68, 63, 63, 63, 63, 63, 62, 25, 62, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 172, 172, 201, 201, 201, 201, 201, 68, 63, 63, 63, 63, 63, 63, 63, 25, 25, 1, 63, 63, 63, 63, 172, 172, 172, 172] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 661 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450436 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 20, 20, 46, 85, 172, 172, 172, 172, 172, 12, 12, 1, 1, 16, 16, 16, 7, 7, 6, 12, 12, 12, 12, 12, 12, 12, 46, 46, 172, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 46, 47, 48, 49, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 428 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450436 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450436 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450436/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450436 Building REAL300024450437 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450437' /scratch/stefan/7786230/working/building/REAL300024450437 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450437 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450437/0 /scratch/stefan/7786230/working/building/REAL300024450437 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/302 `/scratch/stefan/7786230/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450437/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450437 none COCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 80, 166, 166, 80, 80, 73, 73, 73, 73, 73, 72, 27, 72, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 166, 166, 166, 166, 166, 166, 80, 73, 73, 73, 73, 73, 73, 73, 27, 27, 1, 73, 73, 73, 73] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 862 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450437 none COCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 73, 73, 73, 73, 73, 1, 1, 29, 29, 29, 22, 22, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 73, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 232 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450437 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450437 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450437/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450437 Building REAL300024450438 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450438' /scratch/stefan/7786230/working/building/REAL300024450438 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450438 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450438/0 /scratch/stefan/7786230/working/building/REAL300024450438 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/303 `/scratch/stefan/7786230/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450438/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450438 none CC1C(NC(=O)CCC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 32, 32, 8, 32, 4, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 48, 48, 102, 136, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 32, 8, 8, 4, 4, 1, 1, 39, 39, 39, 39, 39, 39, 102, 102, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 586 number of broken/clashed sets: 42 ./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: REAL300024450438 none CC1C(NC(=O)CCC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 55, 55, 74, 74, 74, 167, 182, 201, 201, 201, 201, 55, 55, 55, 53, 32, 53, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 74, 167, 167, 182, 182, 201, 201, 55, 55, 55, 55, 55, 55, 32, 32, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 773 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450438 none CC1C(NC(=O)CCC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 25, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 10, 17, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 4, 18, 18, 25, 25, 39, 39, 1, 1, 1, 1, 1, 1, 10, 10, 55] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450438 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450438 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450438/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450438 Building REAL300024450439 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450439' /scratch/stefan/7786230/working/building/REAL300024450439 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450439 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450439/0 /scratch/stefan/7786230/working/building/REAL300024450439 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/304 `/scratch/stefan/7786230/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450439/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450439 none CC1C(NC(=O)C2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 27, 42, 79, 79, 79, 79, 79, 7, 7, 7, 7, 7, 5, 2, 2, 2, 1, 7, 7, 7, 7, 7, 7, 27, 27, 79] 79 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 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, 44]) total number of confs: 187 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: REAL300024450439 none CC1C(NC(=O)C2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 79, 79, 79, 79, 79, 79, 79, 79, 76, 76, 76, 73, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 79, 79, 79, 79, 79, 76, 76, 76, 76, 76, 76, 39, 39, 1] 79 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 262 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450439 none CC1C(NC(=O)C2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 15, 30, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 4, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 15, 15, 76] 79 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450439 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450439 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450439/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450439 Building REAL300024450440 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450440' /scratch/stefan/7786230/working/building/REAL300024450440 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450440 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450440/0 /scratch/stefan/7786230/working/building/REAL300024450440 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/305 `/scratch/stefan/7786230/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1) `REAL300024450440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450440/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450440 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 35, 130, 130, 130, 130, 130, 1, 1, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 130, 1, 2, 2, 2, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 218 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: REAL300024450440 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 137, 137, 137, 130, 130, 130, 130, 130, 126, 61, 126, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 137, 130, 130, 130, 130, 130, 130, 130, 61, 61, 1, 130, 130, 130, 130, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45]) total number of confs: 552 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450440 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 9, 9, 9, 9, 9, 15, 15, 47, 104, 201, 201, 201, 201, 201, 9, 9, 1, 1, 2, 2, 2, 1, 5, 9, 9, 9, 9, 9, 9, 9, 47, 47, 201, 9, 9, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 426 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450440 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450440 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450440/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450440 Building REAL300024450441 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450441' /scratch/stefan/7786230/working/building/REAL300024450441 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450441 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450441/0 /scratch/stefan/7786230/working/building/REAL300024450441 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/306 `/scratch/stefan/7786230/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450441/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450441 none CC1C(NC(=O)C2(C)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 37, 98, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 37, 37, 201] 201 rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 403 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: REAL300024450441 none CC1C(NC(=O)C2(C)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [119, 119, 119, 119, 122, 122, 122, 201, 201, 201, 201, 201, 201, 119, 119, 119, 115, 51, 115, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 51, 51, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 686 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450441 none CC1C(NC(=O)C2(C)CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 13, 38, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 119] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450441 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450441 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450441/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450441 Building REAL300024450442 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450442' /scratch/stefan/7786230/working/building/REAL300024450442 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450442 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450442/0 /scratch/stefan/7786230/working/building/REAL300024450442 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/307 `/scratch/stefan/7786230/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450442/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450442 none CC(C)CC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 196, 201, 84, 84, 84, 76, 76, 76, 76, 76, 74, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 84, 76, 76, 76, 76, 76, 76, 76, 28, 28, 1, 76, 76, 76, 76] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 767 number of broken/clashed sets: 102 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450442 none CC(C)CC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 30, 30, 28, 18, 28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 76, 76, 76, 76, 76, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 28, 28, 28, 28, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 76, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 251 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450442 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450442 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450442/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450442 Building REAL300024450443 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450443' /scratch/stefan/7786230/working/building/REAL300024450443 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450443 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450443/0 /scratch/stefan/7786230/working/building/REAL300024450443 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/308 `/scratch/stefan/7786230/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450443/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450443 none CC1=CN=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 39, 39, 39, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 47, 47, 47, 47, 47, 1, 1, 39, 39, 39, 39, 39, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 47, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 178 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: REAL300024450443 none CC1=CN=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 158, 62, 62, 62, 47, 47, 47, 47, 47, 46, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 158, 158, 62, 47, 47, 47, 47, 47, 47, 47, 27, 27, 1, 47, 47, 47, 47] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 696 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450443 none CC1=CN=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 29, 29, 29, 39, 39, 39, 39, 39, 62, 62, 85, 127, 201, 201, 201, 201, 201, 39, 39, 2, 2, 2, 1, 1, 5, 5, 29, 39, 39, 39, 39, 39, 39, 39, 85, 85, 201, 39, 39, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 555 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450443 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450443/1 /scratch/stefan/7786230/working/building/REAL300024450443 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/309 `/scratch/stefan/7786230/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C[NH+]=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450443.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450443/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450443 none CC1=C[NH+]=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 47, 47, 47, 47, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 69, 69, 69, 69, 69, 1, 1, 47, 47, 47, 47, 47, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 69, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 231 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: REAL300024450443 none CC1=C[NH+]=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 175, 99, 99, 99, 69, 69, 69, 69, 69, 64, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 175, 175, 99, 69, 69, 69, 69, 69, 69, 69, 27, 27, 1, 69, 69, 69, 69] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 734 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450443 none CC1=C[NH+]=CN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 30, 30, 30, 47, 47, 47, 47, 47, 72, 72, 105, 141, 201, 201, 201, 201, 201, 47, 47, 2, 2, 2, 1, 1, 6, 6, 30, 47, 47, 47, 47, 47, 47, 47, 105, 105, 201, 47, 47, 47, 47] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 571 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450443 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450443 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450443/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450443/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450443 Building REAL300024450444 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450444' /scratch/stefan/7786230/working/building/REAL300024450444 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450444 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450444/0 /scratch/stefan/7786230/working/building/REAL300024450444 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/310 `/scratch/stefan/7786230/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450444/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450444 none CC1C(NC(=O)CCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 37, 60, 60, 60, 171, 189, 201, 201, 37, 37, 37, 37, 33, 37, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 60, 171, 171, 201, 201, 201, 37, 37, 37, 37, 37, 37, 33, 33, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 896 number of broken/clashed sets: 77 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450444 none CC1C(NC(=O)CCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 30, 57, 57, 1, 1, 1, 1, 1, 3, 3, 6, 9, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 4, 20, 20, 37, 37, 52, 1, 1, 1, 1, 1, 1, 6, 6, 37] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 342 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450444 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450444 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450444/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450444 Building REAL300024450445 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450445' /scratch/stefan/7786230/working/building/REAL300024450445 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450445 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450445/0 /scratch/stefan/7786230/working/building/REAL300024450445 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/311 `/scratch/stefan/7786230/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450445/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450445 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 91, 91, 91, 91, 91, 1, 1, 10, 10, 10, 36, 36, 36, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 91, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 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: REAL300024450445 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 174, 109, 109, 109, 91, 91, 91, 91, 91, 82, 30, 82, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 174, 174, 174, 201, 201, 201, 201, 201, 109, 91, 91, 91, 91, 91, 91, 91, 30, 30, 1, 91, 91, 91, 91, 174, 174, 174, 174, 174, 174] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 693 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450445 none COCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 6, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 18, 18, 53, 93, 174, 174, 174, 174, 174, 10, 10, 1, 1, 1, 14, 14, 14, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 53, 53, 174, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 434 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450445 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450445 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450445/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450445 Building REAL300024450446 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450446' /scratch/stefan/7786230/working/building/REAL300024450446 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450446 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450446/0 /scratch/stefan/7786230/working/building/REAL300024450446 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/312 `/scratch/stefan/7786230/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450446/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450446 none CC(CC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [190, 79, 190, 201, 201, 201, 79, 79, 47, 47, 47, 47, 47, 45, 38, 45, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 190, 190, 190, 190, 201, 201, 201, 79, 47, 47, 47, 47, 47, 47, 47, 38, 38, 1, 47, 47, 47, 47] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 825 number of broken/clashed sets: 91 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450446 none CC(CC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 6, 30, 48, 67, 67, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 47, 47, 47, 47, 47, 1, 1, 30, 30, 30, 30, 49, 49, 67, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 386 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450446 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450446 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450446/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450446 Building REAL300024450447 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450447' /scratch/stefan/7786230/working/building/REAL300024450447 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450447 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450447/0 /scratch/stefan/7786230/working/building/REAL300024450447 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/313 `/scratch/stefan/7786230/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450447/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450447 none CC1C(NC(=O)CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 4, 12, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 17, 17, 18, 18, 23, 23, 23, 23, 23, 16, 16, 16, 16, 16, 12, 4, 4, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 18, 18, 23] 23 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 10 ./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: REAL300024450447 none CC1C(NC(=O)CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 10, 10, 10, 20, 23, 23, 23, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 20, 20, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 1] 23 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450447 none CC1C(NC(=O)CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 13, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 3, 13, 13, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 5, 5, 8] 23 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450447 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450447 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450447/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450447 Building REAL300024450448 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450448' /scratch/stefan/7786230/working/building/REAL300024450448 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450448 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450448/0 /scratch/stefan/7786230/working/building/REAL300024450448 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/314 `/scratch/stefan/7786230/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450448/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450448 none CC1C(NC(=O)C2(C)CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 44, 101, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 44, 44, 201] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 411 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: REAL300024450448 none CC1C(NC(=O)C2(C)CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 127, 127, 127, 201, 201, 201, 201, 201, 201, 117, 117, 117, 114, 58, 114, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 127, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 58, 58, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 649 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450448 none CC1C(NC(=O)C2(C)CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 13, 37, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 117] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450448 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450448 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450448/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450448 Building REAL300024450449 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450449' /scratch/stefan/7786230/working/building/REAL300024450449 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450449 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450449/0 /scratch/stefan/7786230/working/building/REAL300024450449 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/315 `/scratch/stefan/7786230/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450449/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450449 none CC1C(NC(=O)C2(C)CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 45, 102, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 45, 45, 201] 201 rigid atoms, others: [43, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 426 number of broken/clashed sets: 27 ./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: REAL300024450449 none CC1C(NC(=O)C2(C)CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 102, 102, 102, 110, 110, 110, 201, 201, 201, 201, 201, 201, 102, 102, 102, 97, 44, 97, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 102, 44, 44, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 637 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450449 none CC1C(NC(=O)C2(C)CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 13, 34, 102, 102, 102, 102, 102, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 102] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450449 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450449 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450449/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450449 Building REAL300024450450 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450450' /scratch/stefan/7786230/working/building/REAL300024450450 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450450 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450450/0 /scratch/stefan/7786230/working/building/REAL300024450450 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/316 `/scratch/stefan/7786230/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CCF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450450/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450450 none CC1C(NC(=O)C2(CCF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 6, 6, 1, 6, 1, 1, 7, 16, 1, 1, 15, 15, 15, 15, 15, 22, 22, 52, 80, 145, 145, 145, 145, 145, 15, 15, 15, 15, 15, 6, 7, 7, 16, 16, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 52, 52, 145] 201 rigid atoms, others: [36, 37, 6, 7, 10, 11, 4, 38, 39] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 429 number of broken/clashed sets: 87 ./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: REAL300024450450 none CC1C(NC(=O)C2(CCF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 51, 51, 51, 91, 91, 91, 145, 201, 201, 145, 145, 51, 51, 51, 49, 42, 49, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 91, 201, 201, 201, 201, 145, 145, 145, 145, 51, 51, 51, 51, 51, 51, 42, 42, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 827 number of broken/clashed sets: 87 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450450 none CC1C(NC(=O)C2(CCF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 15, 41, 48, 15, 15, 1, 1, 1, 1, 1, 3, 3, 9, 17, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 6, 41, 41, 48, 48, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 51] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 287 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450450 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450450 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450450/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450450 Building REAL300024450451 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450451' /scratch/stefan/7786230/working/building/REAL300024450451 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450451 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450451/0 /scratch/stefan/7786230/working/building/REAL300024450451 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/317 `/scratch/stefan/7786230/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450451/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450451 none COCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 123, 189, 189, 65, 65, 65, 59, 59, 59, 59, 59, 57, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 189, 189, 189, 189, 189, 189, 123, 123, 65, 59, 59, 59, 59, 59, 59, 59, 25, 25, 1, 59, 59, 59, 59] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 898 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450451 none COCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 24, 18, 8, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 59, 59, 59, 59, 59, 1, 1, 27, 27, 27, 24, 24, 18, 18, 18, 18, 18, 18, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450451 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450451 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450451/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450451 Building REAL300024450452 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450452' /scratch/stefan/7786230/working/building/REAL300024450452 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450452 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450452/0 /scratch/stefan/7786230/working/building/REAL300024450452 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/318 `/scratch/stefan/7786230/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450452/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450452 none CC1C(NC(=O)COCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 57, 57, 75, 75, 75, 149, 173, 201, 201, 201, 57, 57, 57, 56, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 75, 149, 149, 201, 201, 201, 57, 57, 57, 57, 57, 57, 27, 27, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 766 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450452 none CC1C(NC(=O)COCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 18, 26, 38, 38, 1, 1, 1, 1, 1, 3, 3, 9, 16, 57, 57, 57, 57, 57, 2, 2, 2, 1, 1, 3, 9, 9, 26, 26, 38, 1, 1, 1, 1, 1, 1, 9, 9, 57] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 251 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450452 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450452 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450452/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450452 Building REAL300024450453 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450453' /scratch/stefan/7786230/working/building/REAL300024450453 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450453 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450453/0 /scratch/stefan/7786230/working/building/REAL300024450453 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/319 `/scratch/stefan/7786230/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450453/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450453 none CC1C(NC(=O)CC2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 52, 52, 102, 140, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 15, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 31, 31, 31, 31, 102, 102, 201] 201 rigid atoms, others: [45, 11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 13, 44, 40, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 574 number of broken/clashed sets: 23 ./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: REAL300024450453 none CC1C(NC(=O)CC2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 106, 106, 106, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 96, 30, 96, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 106, 30, 30, 1] 201 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 698 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450453 none CC1C(NC(=O)CC2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 12, 23, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 6, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 12, 12, 106] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 274 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450453 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450453/1 /scratch/stefan/7786230/working/building/REAL300024450453 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/320 `/scratch/stefan/7786230/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450453.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450453/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450453 none CC1C(NC(=O)CC2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 38, 38, 80, 124, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 10, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 80, 80, 201] 201 rigid atoms, others: [45, 11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 13, 44, 40, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 522 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: REAL300024450453 none CC1C(NC(=O)CC2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [119, 119, 119, 119, 161, 161, 161, 197, 201, 201, 201, 201, 201, 201, 119, 119, 119, 109, 33, 109, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 161, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 33, 33, 1] 201 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 706 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450453 none CC1C(NC(=O)CC2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 4, 4, 13, 30, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 6, 19, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 13, 13, 119] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 274 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450453 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450453 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450453/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450453/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450453 Building REAL300024450454 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450454' /scratch/stefan/7786230/working/building/REAL300024450454 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450454 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450454/0 /scratch/stefan/7786230/working/building/REAL300024450454 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/321 `/scratch/stefan/7786230/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450454/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450454 none CC1C(NC(=O)CC2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 44, 44, 87, 126, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 26, 5, 5, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 87, 87, 201] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47, 48]) total number of confs: 534 number of broken/clashed sets: 22 ./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: REAL300024450454 none CC1C(NC(=O)CC2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [74, 74, 74, 74, 84, 84, 84, 162, 201, 201, 201, 201, 201, 74, 74, 74, 68, 25, 68, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 84, 162, 162, 201, 201, 201, 201, 201, 74, 74, 74, 74, 74, 74, 25, 25, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 661 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450454 none CC1C(NC(=O)CC2=CN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 23, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 3, 16, 16, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 74] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450454 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450454 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450454/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450454 Building REAL300024450455 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450455' /scratch/stefan/7786230/working/building/REAL300024450455 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450455 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450455/0 /scratch/stefan/7786230/working/building/REAL300024450455 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/322 `/scratch/stefan/7786230/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450455/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450455 none CCN1C=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 29, 100, 100, 100, 100, 100, 1, 1, 10, 18, 18, 18, 18, 18, 10, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 100, 1, 2, 2, 2, 10] 186 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 34 ./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: REAL300024450455 none CCN1C=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [186, 131, 131, 131, 131, 119, 119, 119, 100, 100, 100, 100, 100, 92, 41, 92, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 131, 186, 186, 186, 186, 186, 131, 119, 100, 100, 100, 100, 100, 100, 100, 41, 41, 1, 100, 100, 100, 100, 131] 186 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 737 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450455 none CCN1C=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 14, 14, 40, 61, 131, 131, 131, 131, 131, 10, 10, 1, 4, 4, 4, 4, 4, 1, 5, 10, 10, 10, 10, 10, 10, 10, 40, 40, 131, 10, 10, 10, 10, 1] 186 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 309 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450455 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450455 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450455/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450455 Building REAL300024450456 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450456' /scratch/stefan/7786230/working/building/REAL300024450456 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450456 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450456/0 /scratch/stefan/7786230/working/building/REAL300024450456 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/323 `/scratch/stefan/7786230/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450456/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450456 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [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, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 11 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450456 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 11, 40, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 34 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450456 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450456 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450456/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450456 Building REAL300024450457 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450457' /scratch/stefan/7786230/working/building/REAL300024450457 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450457 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450457/0 /scratch/stefan/7786230/working/building/REAL300024450457 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/324 `/scratch/stefan/7786230/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C3CC3)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450457/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450457 none CC1C(NC(=O)C2(C3CC3)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [43, 4, 38, 6, 7, 40, 41, 10, 11, 12, 39, 42] set([0, 1, 2, 3, 5, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 13 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.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: REAL300024450457 none CC1C(NC(=O)C2(C3CC3)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 7 number of broken/clashed sets: 1 ./output.4.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: REAL300024450457 none CC1C(NC(=O)C2(C3CC3)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 7 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450457 none CC1C(NC(=O)C2(C3CC3)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 19 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450457 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450457 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450457/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450457 Building REAL300024450458 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450458' /scratch/stefan/7786230/working/building/REAL300024450458 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450458 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450458/0 /scratch/stefan/7786230/working/building/REAL300024450458 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/325 `/scratch/stefan/7786230/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450458/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450458 none CC1C(NC(=O)C(C)(C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 18, 7, 18, 1, 7, 7, 1, 1, 1, 1, 29, 29, 29, 29, 29, 39, 39, 70, 114, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 70, 70, 201] 201 rigid atoms, others: [43, 6, 39, 40, 9, 10, 11, 12, 45, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 507 number of broken/clashed sets: 152 ./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: REAL300024450458 none CC1C(NC(=O)C(C)(C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 49, 49, 49, 150, 150, 150, 201, 201, 201, 44, 44, 44, 43, 21, 43, 11, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 49, 150, 150, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 44, 44, 44, 44, 44, 44, 21, 21, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 765 number of broken/clashed sets: 152 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450458 none CC1C(NC(=O)C(C)(C)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 12, 12, 12, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 9, 15, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 9, 9, 44] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450458 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450458 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450458/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450458 Building REAL300024450459 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450459' /scratch/stefan/7786230/working/building/REAL300024450459 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450459 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450459/0 /scratch/stefan/7786230/working/building/REAL300024450459 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/326 `/scratch/stefan/7786230/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1) `REAL300024450459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450459/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450459 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 170, 119, 119, 119, 93, 93, 93, 93, 93, 90, 44, 90, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 170, 201, 201, 201, 170, 170, 170, 170, 119, 93, 93, 93, 93, 93, 93, 93, 44, 44, 1, 93, 93, 93, 93, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 763 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: REAL300024450459 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 5, 21, 21, 21, 30, 30, 30, 30, 30, 41, 41, 76, 117, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 1, 8, 8, 8, 5, 21, 30, 30, 30, 30, 30, 30, 30, 76, 76, 201, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 503 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450459 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 93, 93, 93, 93, 93, 1, 1, 15, 30, 30, 30, 19, 19, 19, 15, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 93, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450459 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450459 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450459/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450459 Building REAL300024450460 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450460' /scratch/stefan/7786230/working/building/REAL300024450460 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450460 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450460/0 /scratch/stefan/7786230/working/building/REAL300024450460 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/327 `/scratch/stefan/7786230/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450460/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450460 none CC1C(NC(=O)C2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 48, 102, 190, 190, 190, 190, 190, 10, 10, 10, 10, 10, 6, 1, 10, 10, 10, 10, 10, 10, 48, 48, 190] 190 rigid atoms, others: [4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 398 number of broken/clashed sets: 23 ./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: REAL300024450460 none CC1C(NC(=O)C2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 183, 183, 183, 190, 190, 190, 190, 177, 177, 177, 172, 70, 172, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 183, 190, 177, 177, 177, 177, 177, 177, 70, 70, 1] 190 rigid atoms, others: [40, 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]) total number of confs: 561 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450460 none CC1C(NC(=O)C2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 9, 1, 1, 1, 1, 1, 3, 3, 15, 56, 177, 177, 177, 177, 177, 2, 2, 2, 1, 1, 5, 10, 1, 1, 1, 1, 1, 1, 15, 15, 177] 190 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 11, 12, 13, 14, 15, 34, 35, 28, 29, 37] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 38, 39, 40]) total number of confs: 292 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450460 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450460 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450460/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450460 Building REAL300024450461 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450461' /scratch/stefan/7786230/working/building/REAL300024450461 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450461 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450461/0 /scratch/stefan/7786230/working/building/REAL300024450461 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/328 `/scratch/stefan/7786230/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450461/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450461 none CC1C(NC(=O)C2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 43, 100, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 43, 43, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 422 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: REAL300024450461 none CC1C(NC(=O)C2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 104, 104, 104, 201, 201, 201, 201, 201, 98, 98, 98, 97, 46, 97, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 46, 46, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 633 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450461 none CC1C(NC(=O)C2(C)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 12, 34, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 98] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450461 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450461 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450461/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450461 Building REAL300024450462 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450462' /scratch/stefan/7786230/working/building/REAL300024450462 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450462 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450462/0 /scratch/stefan/7786230/working/building/REAL300024450462 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/329 `/scratch/stefan/7786230/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450462/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450462 none CC1C(NC(=O)C2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 52, 110, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 4, 1, 1, 9, 9, 9, 9, 9, 9, 52, 52, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 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: REAL300024450462 none CC1C(NC(=O)C2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [149, 149, 149, 149, 192, 192, 192, 201, 201, 201, 201, 149, 149, 149, 145, 62, 145, 13, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 192, 201, 201, 149, 149, 149, 149, 149, 149, 62, 62, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 611 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450462 none CC1C(NC(=O)C2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 16, 50, 149, 149, 149, 149, 149, 2, 2, 2, 1, 1, 6, 9, 9, 1, 1, 1, 1, 1, 1, 16, 16, 149] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450462 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450462 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450462/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450462 Building REAL300024450463 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450463' /scratch/stefan/7786230/working/building/REAL300024450463 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450463 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450463/0 /scratch/stefan/7786230/working/building/REAL300024450463 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/330 `/scratch/stefan/7786230/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCN2C=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450463/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450463 none CC1C(NC(=O)CCN2C=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 38, 38, 12, 37, 5, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 67, 67, 114, 143, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 38, 13, 13, 5, 5, 1, 1, 1, 43, 43, 43, 43, 43, 43, 114, 114, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 23 ./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: REAL300024450463 none CC1C(NC(=O)CCN2C=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 46, 46, 51, 51, 51, 134, 140, 201, 201, 201, 201, 46, 46, 46, 46, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 51, 134, 134, 140, 140, 201, 201, 201, 46, 46, 46, 46, 46, 46, 27, 27, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 661 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450463 none CC1C(NC(=O)CCN2C=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 19, 43, 43, 43, 43, 1, 1, 1, 1, 1, 3, 3, 11, 17, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 3, 13, 13, 19, 19, 43, 43, 43, 1, 1, 1, 1, 1, 1, 11, 11, 46] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450463 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450463 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450463/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450463 Building REAL300024450464 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450464' /scratch/stefan/7786230/working/building/REAL300024450464 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450464 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450464/0 /scratch/stefan/7786230/working/building/REAL300024450464 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/331 `/scratch/stefan/7786230/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450464/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450464 none CC1=NN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 37, 116, 116, 116, 116, 116, 1, 1, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 116, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 31 ./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: REAL300024450464 none CC1=NN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 123, 123, 123, 116, 116, 116, 116, 116, 112, 54, 112, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 123, 116, 116, 116, 116, 116, 116, 116, 54, 54, 1, 116, 116, 116, 116] 201 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 509 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450464 none CC1=NN=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 12, 12, 12, 12, 12, 19, 19, 62, 121, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 1, 1, 9, 12, 12, 12, 12, 12, 12, 12, 62, 62, 201, 12, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 473 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450464 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450464 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450464/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450464 Building REAL300024450465 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450465' /scratch/stefan/7786230/working/building/REAL300024450465 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450465 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450465/0 /scratch/stefan/7786230/working/building/REAL300024450465 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/332 `/scratch/stefan/7786230/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C(C)O1) `REAL300024450465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450465/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450465 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C(C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 29, 82, 82, 82, 82, 82, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 82, 1, 2, 2, 2, 15, 15, 15, 15] 164 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 31 ./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: REAL300024450465 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C(C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 96, 96, 96, 82, 82, 82, 82, 82, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 96, 82, 82, 82, 82, 82, 82, 82, 39, 39, 1, 82, 82, 82, 82, 164, 164, 164, 164] 164 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 522 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450465 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C(C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 15, 15, 15, 15, 15, 21, 21, 73, 106, 164, 164, 164, 164, 164, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 73, 73, 164, 15, 15, 15, 15, 1, 2, 2, 2] 164 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 442 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450465 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450465 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450465/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450465 Building REAL300024450466 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450466' /scratch/stefan/7786230/working/building/REAL300024450466 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450466 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450466/0 /scratch/stefan/7786230/working/building/REAL300024450466 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/333 `/scratch/stefan/7786230/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]2C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450466/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450466 none CC1C(NC(=O)[C@@H]2C[C@H]2C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 22, 28, 28, 55, 77, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 11, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 55, 55, 201] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 440 number of broken/clashed sets: 39 ./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: REAL300024450466 none CC1C(NC(=O)[C@@H]2C[C@H]2C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 75, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 63, 37, 63, 12, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 68, 37, 37, 1] 201 rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 622 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450466 none CC1C(NC(=O)[C@@H]2C[C@H]2C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 22, 22, 22, 22, 22, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 9, 16, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 5, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 9, 9, 68] 201 rigid atoms, others: [0, 1, 2, 3, 48, 33, 19, 32, 50, 46, 15, 16, 17, 18, 51, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450466 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450466 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450466/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450466 Building REAL300024450467 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450467' /scratch/stefan/7786230/working/building/REAL300024450467 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450467 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450467/0 /scratch/stefan/7786230/working/building/REAL300024450467 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/334 `/scratch/stefan/7786230/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450467/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450467 none CC1CC1C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 11, 11, 11, 18, 18, 18, 18, 18, 28, 28, 66, 103, 186, 186, 186, 186, 186, 18, 18, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 18, 18, 18, 18, 18, 18, 18, 66, 66, 186, 18, 18, 18, 18] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 3, 36, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 468 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.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: REAL300024450467 none CC1CC1C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 186, 186, 186, 80, 80, 80, 71, 71, 71, 71, 71, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 186, 80, 71, 71, 71, 71, 71, 71, 71, 28, 28, 1, 71, 71, 71, 71] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 616 number of broken/clashed sets: 12 ./output.4.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: REAL300024450467 none CC1CC1C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 17, 71, 71, 71, 71, 71, 1, 1, 32, 32, 32, 32, 32, 32, 32, 18, 18, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 71, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 210 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450467 none CC1CC1C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 24, 24, 24, 32, 32, 32, 32, 32, 48, 48, 87, 130, 201, 201, 201, 201, 201, 32, 32, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 24, 32, 32, 32, 32, 32, 32, 32, 87, 87, 201, 32, 32, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 541 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450467 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450467 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450467/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450467 Building REAL300024450468 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450468' /scratch/stefan/7786230/working/building/REAL300024450468 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450468 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450468/0 /scratch/stefan/7786230/working/building/REAL300024450468 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/335 `/scratch/stefan/7786230/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1) `REAL300024450468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450468/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450468 none CCC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 19, 67, 67, 67, 67, 67, 1, 1, 10, 10, 25, 25, 25, 25, 25, 10, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 1, 2, 2, 2] 128 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 208 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: REAL300024450468 none CCC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 95, 95, 95, 82, 82, 82, 67, 67, 67, 67, 67, 65, 39, 65, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 95, 95, 128, 128, 128, 128, 128, 95, 82, 67, 67, 67, 67, 67, 67, 67, 39, 39, 1, 67, 67, 67, 67] 128 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 506 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450468 none CCC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 14, 14, 34, 44, 95, 95, 95, 95, 95, 10, 10, 1, 1, 7, 7, 7, 6, 6, 1, 5, 10, 10, 10, 10, 10, 10, 10, 34, 34, 95, 10, 10, 10, 10] 128 rigid atoms, others: [32, 1, 2, 3, 4, 5, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450468 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450468 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450468/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450468 Building REAL300024450469 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450469' /scratch/stefan/7786230/working/building/REAL300024450469 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450469 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450469/0 /scratch/stefan/7786230/working/building/REAL300024450469 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/336 `/scratch/stefan/7786230/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450469/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450469 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 167, 58, 58, 58, 50, 50, 50, 50, 50, 48, 24, 48, 11, 1, 1, 1, 1, 1, 1, 1, 50, 50, 200, 201, 201, 201, 201, 201, 201, 201, 200, 167, 167, 58, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 50, 50, 50, 50, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] 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, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 824 number of broken/clashed sets: 76 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450469 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 26, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 50, 50, 50, 50, 50, 1, 1, 28, 34, 34, 32, 32, 32, 32, 31, 28, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 1, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 46, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 276 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450469 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450469 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450469/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450469 Building REAL300024450470 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450470' /scratch/stefan/7786230/working/building/REAL300024450470 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450470 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450470/0 /scratch/stefan/7786230/working/building/REAL300024450470 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/337 `/scratch/stefan/7786230/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450470/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450470 none CC1C(NC(=O)CCCC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 17, 17, 17, 27, 22, 28, 29, 29, 29, 29, 15, 15, 15, 15, 10, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 17, 27, 27, 27, 27, 27, 28, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 15, 10, 10, 1] 29 rigid atoms, others: [56, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 128 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450470 none CC1C(NC(=O)CCCC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 11, 7, 12, 15, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 11, 12, 15, 15, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 7, 7, 15] 29 rigid atoms, others: [0, 1, 2, 3, 49, 16, 32, 18, 14, 15, 48, 17, 50, 51, 52, 53, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450470 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450470 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450470/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450470 Building REAL300024450471 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450471' /scratch/stefan/7786230/working/building/REAL300024450471 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450471 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450471/0 /scratch/stefan/7786230/working/building/REAL300024450471 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/338 `/scratch/stefan/7786230/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450471/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450471 none CC1C(NC(=O)[C@@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 22, 22, 55, 100, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 55, 55, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 451 number of broken/clashed sets: 10 ./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: REAL300024450471 none CC1C(NC(=O)[C@@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 101, 101, 101, 134, 134, 134, 201, 201, 201, 201, 201, 201, 101, 101, 101, 96, 42, 96, 12, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 134, 201, 201, 201, 201, 201, 101, 101, 101, 101, 101, 101, 42, 42, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 645 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450471 none CC1C(NC(=O)[C@@H]2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 34, 101, 101, 101, 101, 101, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 101] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450471 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450471 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450471/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450471 Building REAL300024450472 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450472' /scratch/stefan/7786230/working/building/REAL300024450472 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450472 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450472/0 /scratch/stefan/7786230/working/building/REAL300024450472 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/339 `/scratch/stefan/7786230/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450472/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450472 none C[C@H]1CC[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 26, 26, 26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 61, 61, 61, 61, 61, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 61, 1, 2, 2, 2, 26, 26, 26, 26] 201 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 41 ./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: REAL300024450472 none C[C@H]1CC[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 201, 73, 73, 61, 61, 61, 61, 61, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 61, 61, 61, 61, 61, 61, 61, 36, 36, 1, 61, 61, 61, 61, 201, 201, 201, 201] 201 rigid atoms, others: [46, 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, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 613 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450472 none C[C@H]1CC[C@H](C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 26, 26, 26, 26, 26, 38, 38, 90, 127, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26, 26, 26, 26, 26, 90, 90, 201, 26, 26, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 5, 34, 35, 52, 53, 54, 51, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 549 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450472 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450472 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450472/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450472 Building REAL300024450473 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450473' /scratch/stefan/7786230/working/building/REAL300024450473 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450473 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450473/0 /scratch/stefan/7786230/working/building/REAL300024450473 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/340 `/scratch/stefan/7786230/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450473/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450473 none CC(C)C(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 12 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450473 none CC(C)C(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 6, 6, 6, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4] 6 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 12, 47, 43, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 36 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450473 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450473 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450473/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450473 Building REAL300024450474 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450474' /scratch/stefan/7786230/working/building/REAL300024450474 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450474 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450474/0 /scratch/stefan/7786230/working/building/REAL300024450474 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/341 `/scratch/stefan/7786230/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450474/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450474 none CCC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 115, 77, 77, 77, 59, 59, 59, 59, 59, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 115, 115, 77, 59, 59, 59, 59, 59, 59, 59, 30, 30, 1, 59, 59, 59, 59] 116 rigid atoms, others: [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, 48, 49, 50, 51, 53, 54, 55, 56]) total number of confs: 458 number of broken/clashed sets: 52 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450474 none CCC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 12, 12, 12, 12, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 59, 59, 59, 59, 59, 1, 1, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 59, 1, 2, 2, 2] 116 rigid atoms, others: [16, 11, 15, 44, 10, 43, 12, 13, 14, 45, 48, 49, 46, 27, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450474 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450474/1 /scratch/stefan/7786230/working/building/REAL300024450474 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/342 `/scratch/stefan/7786230/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450474.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450474/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450474 none CCC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 102, 72, 72, 72, 50, 50, 50, 50, 50, 42, 25, 42, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 102, 102, 72, 50, 50, 50, 50, 50, 50, 50, 25, 25, 1, 50, 50, 50, 50] 105 rigid atoms, others: [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, 48, 49, 50, 51, 53, 54, 55, 56]) total number of confs: 411 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450474 none CCC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 14, 14, 14, 14, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 50, 50, 50, 50, 50, 1, 1, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 14, 14, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 1, 2, 2, 2] 105 rigid atoms, others: [16, 11, 15, 44, 10, 43, 12, 13, 14, 45, 48, 49, 46, 27, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 169 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450474 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450474 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450474/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450474/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450474 Building REAL300024450475 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450475' /scratch/stefan/7786230/working/building/REAL300024450475 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450475 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450475/0 /scratch/stefan/7786230/working/building/REAL300024450475 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/343 `/scratch/stefan/7786230/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450475/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450475 none CCC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 197, 189, 197, 197, 123, 123, 123, 77, 77, 77, 77, 77, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 189, 189, 123, 77, 77, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77, 77, 77] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 816 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450475 none CCC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 26, 19, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 77, 77, 77, 77, 77, 1, 1, 39, 39, 39, 39, 39, 30, 30, 26, 26, 26, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 77, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 316 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450475 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450475/1 /scratch/stefan/7786230/working/building/REAL300024450475 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/344 `/scratch/stefan/7786230/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450475.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450475/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450475 none CCC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 34, 34, 24, 24, 24, 24, 24, 24, 24, 24, 24, 19, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 33, 33, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 1, 24, 24, 24, 24] 34 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 124 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450475 none CCC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 5, 4, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 24, 24, 24, 24, 24, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 1, 2, 2, 2] 34 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450475 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450475 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450475/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450475/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450475 Building REAL300024450476 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450476' /scratch/stefan/7786230/working/building/REAL300024450476 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450476 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450476/0 /scratch/stefan/7786230/working/building/REAL300024450476 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/345 `/scratch/stefan/7786230/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C) `REAL300024450476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450476/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450476 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 118, 118, 118, 86, 86, 86, 86, 86, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 86, 86, 86, 86, 86, 86, 86, 29, 29, 1, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 807 number of broken/clashed sets: 109 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450476 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 86, 86, 86, 86, 86, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 44, 11, 40, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 238 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450476 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450476 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450476/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450476 Building REAL300024450477 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450477' /scratch/stefan/7786230/working/building/REAL300024450477 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450477 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450477/0 /scratch/stefan/7786230/working/building/REAL300024450477 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/346 `/scratch/stefan/7786230/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1) `REAL300024450477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450477/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450477 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [37, 37, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 50, 50, 50, 50, 50, 1, 1, 37, 37, 37, 37, 37, 37, 21, 21, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 1, 2, 2, 2, 37, 37] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 188 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: REAL300024450477 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 185, 59, 59, 59, 50, 50, 50, 50, 50, 49, 22, 49, 11, 1, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 185, 185, 59, 50, 50, 50, 50, 50, 50, 50, 22, 22, 1, 50, 50, 50, 50, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 715 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450477 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 6, 25, 25, 25, 37, 37, 37, 37, 37, 57, 57, 99, 142, 201, 201, 201, 201, 201, 37, 37, 1, 1, 1, 2, 2, 2, 6, 6, 25, 37, 37, 37, 37, 37, 37, 37, 99, 99, 201, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 603 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450477 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450477 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450477/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450477 Building REAL300024450478 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450478' /scratch/stefan/7786230/working/building/REAL300024450478 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450478 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450478/0 /scratch/stefan/7786230/working/building/REAL300024450478 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/347 `/scratch/stefan/7786230/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450478/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450478 none CC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 39, 117, 117, 117, 117, 117, 1, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 117, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 216 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: REAL300024450478 none CC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 176, 176, 176, 117, 117, 117, 117, 117, 112, 58, 112, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 176, 117, 117, 117, 117, 117, 117, 117, 58, 58, 1, 117, 117, 117, 117] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 601 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450478 none CC1=NNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 17, 17, 17, 17, 17, 23, 23, 60, 113, 201, 201, 201, 201, 201, 17, 17, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 60, 60, 201, 17, 17, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 467 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450478 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450478 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450478/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450478 Building REAL300024450479 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450479' /scratch/stefan/7786230/working/building/REAL300024450479 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450479 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450479/0 /scratch/stefan/7786230/working/building/REAL300024450479 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/348 `/scratch/stefan/7786230/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1) `REAL300024450479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450479/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450479 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 57, 177, 177, 177, 177, 177, 1, 1, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 177, 1, 2, 2, 2, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 300 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: REAL300024450479 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 201, 177, 177, 177, 177, 177, 164, 66, 164, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 177, 66, 66, 1, 177, 177, 177, 177, 201, 201] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 609 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450479 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 7, 7, 7, 7, 7, 14, 14, 49, 108, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 49, 49, 201, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 26, 27, 28, 29, 30] set([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]) total number of confs: 419 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450479 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450479 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450479/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450479 Building REAL300024450480 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450480' /scratch/stefan/7786230/working/building/REAL300024450480 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450480 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450480/0 /scratch/stefan/7786230/working/building/REAL300024450480 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/349 `/scratch/stefan/7786230/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NN=N1) `REAL300024450480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450480/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450480 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NN=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 62, 62, 62, 62, 62, 1, 1, 12, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 1, 2, 2, 2, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 32 ./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: REAL300024450480 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NN=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 72, 72, 72, 62, 62, 62, 62, 62, 61, 34, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 72, 62, 62, 62, 62, 62, 62, 62, 34, 34, 1, 62, 62, 62, 62, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 416 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450480 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NN=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 9, 9, 9, 13, 13, 13, 13, 13, 17, 17, 48, 91, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 48, 48, 201, 13, 13, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 431 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450480 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450480/1 /scratch/stefan/7786230/working/building/REAL300024450480 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/350 `/scratch/stefan/7786230/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450480.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450480/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450480 none CC1=NNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 46, 151, 151, 151, 151, 151, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 151, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 254 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: REAL300024450480 none CC1=NNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 201, 151, 151, 151, 151, 151, 147, 60, 147, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 151, 60, 60, 1, 151, 151, 151, 151] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 607 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450480 none CC1=NNN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 48, 105, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 3, 9, 9, 9, 9, 9, 9, 9, 48, 48, 201, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 430 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450480 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450480 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450480/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450480/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450480 Building REAL300024450481 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450481' /scratch/stefan/7786230/working/building/REAL300024450481 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450481 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450481/0 /scratch/stefan/7786230/working/building/REAL300024450481 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/351 `/scratch/stefan/7786230/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450481/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450481 none CCCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 189, 104, 189, 190, 104, 104, 85, 85, 85, 85, 85, 82, 40, 82, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 189, 190, 190, 190, 104, 85, 85, 85, 85, 85, 85, 85, 40, 40, 1, 85, 85, 85, 85] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 903 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450481 none CCCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 24, 12, 3, 12, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 85, 85, 85, 85, 85, 1, 1, 27, 27, 27, 27, 27, 26, 26, 12, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 85, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 253 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450481 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450481 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450481/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450481 Building REAL300024450482 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450482' /scratch/stefan/7786230/working/building/REAL300024450482 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450482 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450482/0 /scratch/stefan/7786230/working/building/REAL300024450482 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/352 `/scratch/stefan/7786230/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450482/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450482 none C=C(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 201, 201, 110, 110, 67, 67, 67, 67, 67, 66, 42, 66, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 67, 67, 67, 67, 67, 67, 67, 42, 42, 1, 67, 67, 67, 67] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 874 number of broken/clashed sets: 51 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450482 none C=C(C)C(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 21, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 67, 67, 67, 67, 67, 1, 1, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450482 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450482 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450482/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450482 Building REAL300024450483 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450483' /scratch/stefan/7786230/working/building/REAL300024450483 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450483 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450483/0 /scratch/stefan/7786230/working/building/REAL300024450483 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/353 `/scratch/stefan/7786230/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450483/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450483 none CC(CC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 133, 195, 200, 201, 201, 133, 133, 100, 100, 100, 100, 100, 95, 30, 95, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 195, 195, 195, 195, 200, 200, 201, 201, 133, 100, 100, 100, 100, 100, 100, 100, 30, 30, 1, 100, 100, 100, 100] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 768 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450483 none CC(CC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 12, 18, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 100, 100, 100, 100, 100, 1, 1, 12, 12, 12, 12, 18, 18, 36, 36, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 100, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 286 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450483 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450483 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450483/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450483 Building REAL300024450484 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450484' /scratch/stefan/7786230/working/building/REAL300024450484 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450484 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450484/0 /scratch/stefan/7786230/working/building/REAL300024450484 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/354 `/scratch/stefan/7786230/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450484/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450484 none CC1C(NC(=O)C2CCC2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 12, 12, 1, 12, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 21, 21, 58, 84, 151, 151, 151, 151, 151, 17, 17, 17, 17, 17, 12, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 58, 58, 151] 163 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 390 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: REAL300024450484 none CC1C(NC(=O)C2CCC2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 70, 70, 70, 79, 79, 79, 151, 151, 151, 151, 163, 163, 70, 70, 70, 69, 38, 69, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 79, 151, 151, 151, 151, 151, 151, 163, 163, 70, 70, 70, 70, 70, 70, 38, 38, 1] 163 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 519 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450484 none CC1C(NC(=O)C2CCC2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 45, 45, 1, 1, 1, 1, 1, 3, 3, 11, 18, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 3, 17, 17, 17, 17, 17, 17, 45, 45, 1, 1, 1, 1, 1, 1, 11, 11, 70] 163 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450484 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450484 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450484/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450484 Building REAL300024450485 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450485' /scratch/stefan/7786230/working/building/REAL300024450485 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450485 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450485/0 /scratch/stefan/7786230/working/building/REAL300024450485 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/355 `/scratch/stefan/7786230/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450485/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450485 none CC1C(NC(=O)C2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 22, 22, 60, 120, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 60, 60, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 462 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: REAL300024450485 none CC1C(NC(=O)C2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [129, 129, 129, 129, 135, 135, 135, 201, 201, 201, 201, 201, 129, 129, 129, 127, 57, 127, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 135, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 129, 57, 57, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450485 none CC1C(NC(=O)C2CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 13, 38, 129, 129, 129, 129, 129, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 13, 13, 129] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450485 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450485 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450485/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450485 Building REAL300024450486 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450486' /scratch/stefan/7786230/working/building/REAL300024450486 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450486 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450486/0 /scratch/stefan/7786230/working/building/REAL300024450486 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/356 `/scratch/stefan/7786230/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CNC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450486/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450486 none CC1C(NC(=O)C2=CNC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 22, 22, 59, 108, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 9, 1, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15, 59, 59, 201] 201 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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, 44, 45, 46]) total number of confs: 481 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: REAL300024450486 none CC1C(NC(=O)C2=CNC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 114, 114, 114, 201, 201, 201, 201, 201, 201, 84, 84, 84, 82, 46, 82, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 114, 201, 201, 201, 201, 201, 84, 84, 84, 84, 84, 84, 46, 46, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 518 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450486 none CC1C(NC(=O)C2=CNC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 11, 26, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 84] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450486 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450486 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450486/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450486 Building REAL300024450487 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450487' /scratch/stefan/7786230/working/building/REAL300024450487 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450487 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450487/0 /scratch/stefan/7786230/working/building/REAL300024450487 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/357 `/scratch/stefan/7786230/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450487/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450487 none CC1C(NC(=O)C2CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 17, 17, 38, 49, 70, 70, 70, 70, 70, 13, 13, 13, 13, 13, 11, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 13, 38, 38, 70] 70 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 14 ./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: REAL300024450487 none CC1C(NC(=O)C2CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 40, 40, 40, 46, 46, 46, 70, 70, 70, 70, 70, 70, 40, 40, 40, 39, 27, 39, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 46, 70, 70, 70, 70, 70, 70, 70, 40, 40, 40, 40, 40, 40, 27, 27, 1] 70 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 227 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450487 none CC1C(NC(=O)C2CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 10, 16, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 40] 70 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450487 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450487 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450487/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450487 Building REAL300024450488 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450488' /scratch/stefan/7786230/working/building/REAL300024450488 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450488 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450488/0 /scratch/stefan/7786230/working/building/REAL300024450488 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/358 `/scratch/stefan/7786230/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450488/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450488 none C=CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 127, 201, 201, 127, 127, 67, 67, 67, 67, 67, 66, 48, 66, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 67, 67, 67, 67, 67, 67, 67, 48, 48, 1, 67, 67, 67, 67] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 806 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450488 none C=CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 67, 67, 67, 67, 67, 1, 1, 24, 24, 24, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450488 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450488 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450488/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450488 Building REAL300024450489 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450489' /scratch/stefan/7786230/working/building/REAL300024450489 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450489 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450489/0 /scratch/stefan/7786230/working/building/REAL300024450489 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/359 `/scratch/stefan/7786230/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450489/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450489 none C#CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 150, 158, 150, 135, 43, 43, 43, 34, 34, 34, 34, 34, 34, 25, 34, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 201, 197, 197, 158, 158, 158, 158, 158, 158, 135, 135, 43, 34, 34, 34, 34, 34, 34, 34, 25, 25, 1, 34, 34, 34, 34] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 920 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450489 none C#CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 21, 26, 21, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 9, 34, 34, 34, 34, 34, 1, 1, 52, 49, 50, 26, 26, 26, 26, 26, 26, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 34, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450489 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450489 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450489/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450489 Building REAL300024450490 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450490' /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450490 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450490/0 /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/360 `/scratch/stefan/7786230/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450490/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 7] 7 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 27 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: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 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, 1] 7 rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 13 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7] 7 rigid atoms, others: [0, 1, 2, 3, 48, 32, 43, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450490/1 /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/361 `/scratch/stefan/7786230/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450490.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450490/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6] 6 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 23 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: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 6 rigid atoms, others: [51, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 7 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 4, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 6] 6 rigid atoms, others: [0, 1, 2, 3, 48, 32, 43, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 27 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450490/2 /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/362 `/scratch/stefan/7786230/working/3D/362' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450490.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450490/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 55, 106, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 55, 55, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 452 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: REAL300024450490 none CC1C(NC(=O)[C@H]2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 136, 136, 136, 200, 200, 200, 201, 201, 201, 201, 201, 201, 136, 136, 136, 131, 55, 131, 12, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 136, 136, 136, 136, 55, 55, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 616 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450490 none CC1C(NC(=O)[C@H]2CCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 13, 42, 136, 136, 136, 136, 136, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 136] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 243 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450490 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450490 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450490/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450490/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450490/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450490 Building REAL300024450491 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450491' /scratch/stefan/7786230/working/building/REAL300024450491 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450491 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450491/0 /scratch/stefan/7786230/working/building/REAL300024450491 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/363 `/scratch/stefan/7786230/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450491/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450491 none C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 3, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 73, 73, 73, 73, 73, 1, 1, 16, 16, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 73, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 23 ./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: REAL300024450491 none C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 201, 78, 78, 73, 73, 73, 73, 73, 72, 37, 72, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 78, 73, 73, 73, 73, 73, 73, 73, 37, 37, 1, 73, 73, 73, 73] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 605 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450491 none C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 16, 16, 16, 16, 16, 25, 25, 59, 104, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 1, 12, 16, 16, 16, 16, 16, 16, 16, 59, 59, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 452 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450491 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450491 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450491/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450491 Building REAL300024450492 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450492' /scratch/stefan/7786230/working/building/REAL300024450492 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450492 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450492/0 /scratch/stefan/7786230/working/building/REAL300024450492 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/364 `/scratch/stefan/7786230/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450492/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450492 none CC1C(NC(=O)CC2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 22, 22, 6, 22, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 49, 49, 86, 125, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 86, 86, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 550 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: REAL300024450492 none CC1C(NC(=O)CC2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 84, 84, 84, 186, 201, 201, 201, 201, 201, 67, 67, 67, 64, 29, 64, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 84, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 29, 29, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 766 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450492 none CC1C(NC(=O)CC2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 4, 18, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 10, 10, 67] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450492 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450492 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450492/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450492 Building REAL300024450493 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450493' /scratch/stefan/7786230/working/building/REAL300024450493 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450493 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450493/0 /scratch/stefan/7786230/working/building/REAL300024450493 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/365 `/scratch/stefan/7786230/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450493/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450493 none CC1C(NC(=O)C2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 49, 91, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 49, 49, 201] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 439 number of broken/clashed sets: 28 ./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: REAL300024450493 none CC1C(NC(=O)C2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 68, 68, 68, 201, 201, 201, 201, 67, 67, 67, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 38, 38, 1] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 591 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450493 none CC1C(NC(=O)C2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 24, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 67] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450493 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450493 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450493/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450493 Building REAL300024450494 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450494' /scratch/stefan/7786230/working/building/REAL300024450494 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450494 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450494/0 /scratch/stefan/7786230/working/building/REAL300024450494 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/366 `/scratch/stefan/7786230/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450494/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450494 none CC1C(NC(=O)C[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 37, 7, 37, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 37, 37, 37, 37, 39, 39, 72, 114, 201, 201, 201, 201, 201, 37, 37, 37, 37, 37, 37, 7, 7, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 72, 72, 201] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 507 number of broken/clashed sets: 6 ./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.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: REAL300024450494 none CC1C(NC(=O)C[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 48, 48, 144, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 43, 23, 43, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 144, 144, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 48, 23, 23, 1] 201 rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 708 number of broken/clashed sets: 6 ./output.4.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: REAL300024450494 none CC1C(NC(=O)C[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 22, 64, 6, 6, 6, 6, 1, 6, 1, 1, 1, 64, 64, 64, 64, 64, 67, 67, 104, 144, 201, 201, 201, 201, 201, 64, 64, 64, 64, 64, 64, 22, 22, 6, 6, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 104, 104, 201] 201 rigid atoms, others: [39, 40, 41, 10, 43, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 575 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450494 none CC1C(NC(=O)C[C@@H]2C[C@H]2C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 2, 12, 37, 37, 37, 37, 37, 64, 64, 1, 1, 1, 1, 1, 3, 3, 10, 17, 48, 48, 48, 48, 48, 2, 2, 2, 1, 1, 2, 12, 12, 37, 37, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 10, 10, 48] 201 rigid atoms, others: [0, 1, 2, 3, 48, 33, 32, 44, 45, 46, 15, 16, 17, 18, 19, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 300 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450494 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450494 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450494/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450494 Building REAL300024450495 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450495' /scratch/stefan/7786230/working/building/REAL300024450495 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450495 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450495/0 /scratch/stefan/7786230/working/building/REAL300024450495 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/367 `/scratch/stefan/7786230/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450495/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450495 none CC1COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 23, 70, 70, 70, 70, 70, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 70, 1, 2, 2, 2, 14, 14] 146 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 162 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: REAL300024450495 none CC1COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 78, 78, 78, 70, 70, 70, 70, 70, 67, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 146, 146, 146, 146, 146, 146, 146, 146, 78, 70, 70, 70, 70, 70, 70, 70, 39, 39, 1, 70, 70, 70, 70, 146, 146] 146 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 462 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450495 none CC1COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 14, 14, 14, 14, 14, 23, 23, 66, 90, 146, 146, 146, 146, 146, 14, 14, 1, 2, 2, 2, 1, 1, 1, 1, 11, 14, 14, 14, 14, 14, 14, 14, 66, 66, 146, 14, 14, 14, 14, 1, 1] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 401 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450495 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450495 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450495/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450495 Building REAL300024450496 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450496' /scratch/stefan/7786230/working/building/REAL300024450496 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450496 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450496/0 /scratch/stefan/7786230/working/building/REAL300024450496 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/368 `/scratch/stefan/7786230/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@]23C[C@H]2CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450496/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450496 none CC1C(NC(=O)[C@]23C[C@H]2CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 18, 18, 46, 91, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 46, 46, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 423 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: REAL300024450496 none CC1C(NC(=O)[C@]23C[C@H]2CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 69, 69, 69, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 69, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 38, 38, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 404 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450496 none CC1C(NC(=O)[C@]23C[C@H]2CCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 25, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 67] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450496 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450496 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450496/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450496 Building REAL300024450497 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450497' /scratch/stefan/7786230/working/building/REAL300024450497 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450497 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450497/0 /scratch/stefan/7786230/working/building/REAL300024450497 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/369 `/scratch/stefan/7786230/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450497/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450497 none CC[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 23, 23, 23, 23, 23, 23, 5, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 22, 85, 85, 85, 85, 85, 1, 1, 25, 25, 25, 25, 25, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 85, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 49, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 214 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: REAL300024450497 none CC[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 127, 201, 127, 127, 85, 85, 85, 85, 85, 78, 41, 78, 12, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 85, 85, 85, 85, 85, 85, 85, 41, 41, 1, 85, 85, 85, 85] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 660 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450497 none CC[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 10, 10, 10, 23, 23, 23, 23, 23, 34, 34, 84, 123, 201, 201, 201, 201, 201, 23, 23, 3, 3, 3, 3, 3, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 84, 84, 201, 23, 23, 23, 23] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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, 50, 51, 52]) total number of confs: 540 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450497 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450497 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450497/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450497 Building REAL300024450498 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450498' /scratch/stefan/7786230/working/building/REAL300024450498 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450498 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450498/0 /scratch/stefan/7786230/working/building/REAL300024450498 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/370 `/scratch/stefan/7786230/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1) `REAL300024450498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450498/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450498 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [25, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 54, 54, 54, 54, 54, 1, 1, 13, 13, 13, 25, 25, 25, 25, 25, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 180 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: REAL300024450498 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 58, 58, 58, 54, 54, 54, 54, 54, 52, 24, 52, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 58, 54, 54, 54, 54, 54, 54, 54, 24, 24, 1, 54, 54, 54, 54, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 365 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450498 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [5, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 13, 13, 22, 22, 52, 94, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 6, 6, 6, 5, 5, 8, 13, 13, 13, 13, 13, 13, 13, 52, 52, 201, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 468 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450498 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450498 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450498/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450498 Building REAL300024450499 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450499' /scratch/stefan/7786230/working/building/REAL300024450499 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450499 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450499/0 /scratch/stefan/7786230/working/building/REAL300024450499 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/371 `/scratch/stefan/7786230/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450499/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450499 none CC1=NNC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 50, 147, 147, 147, 147, 147, 1, 1, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 147, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 40 ./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: REAL300024450499 none CC1=NNC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 151, 151, 151, 147, 147, 147, 147, 147, 141, 53, 141, 13, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 201, 201, 151, 147, 147, 147, 147, 147, 147, 147, 53, 53, 1, 147, 147, 147, 147] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 546 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450499 none CC1=NNC(C)=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 13, 13, 13, 13, 13, 20, 20, 60, 106, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 60, 60, 201, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 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, 48]) total number of confs: 461 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450499 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450499 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450499/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450499 Building REAL300024450500 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450500' /scratch/stefan/7786230/working/building/REAL300024450500 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450500 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450500/0 /scratch/stefan/7786230/working/building/REAL300024450500 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/372 `/scratch/stefan/7786230/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450500/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450500 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 27, 75, 75, 75, 75, 75, 1, 1, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 75, 1, 2, 2, 2] 156 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 29 ./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: REAL300024450500 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [156, 156, 156, 156, 156, 156, 76, 76, 76, 75, 75, 75, 75, 75, 68, 39, 68, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 156, 156, 156, 156, 156, 156, 76, 75, 75, 75, 75, 75, 75, 75, 39, 39, 1, 75, 75, 75, 75] 156 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 364 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450500 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 13, 19, 19, 64, 96, 156, 156, 156, 156, 156, 13, 13, 2, 2, 2, 1, 1, 1, 10, 13, 13, 13, 13, 13, 13, 13, 64, 64, 156, 13, 13, 13, 13] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 410 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450500 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450500 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450500/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450500 Building REAL300024450501 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450501' /scratch/stefan/7786230/working/building/REAL300024450501 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450501 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450501/0 /scratch/stefan/7786230/working/building/REAL300024450501 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/373 `/scratch/stefan/7786230/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450501/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450501 none CC(C)CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 163, 200, 200, 159, 178, 54, 54, 54, 44, 44, 44, 44, 44, 42, 24, 42, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 200, 201, 201, 200, 201, 201, 201, 200, 200, 197, 197, 178, 178, 54, 44, 44, 44, 44, 44, 44, 44, 24, 24, 1, 44, 44, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 1298 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450501 none CC(C)CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 26, 30, 30, 22, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 44, 44, 44, 44, 44, 1, 1, 31, 31, 30, 31, 31, 30, 31, 31, 31, 30, 30, 27, 27, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 290 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450501 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450501 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450501/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450501 Building REAL300024450502 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450502' /scratch/stefan/7786230/working/building/REAL300024450502 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450502 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450502/0 /scratch/stefan/7786230/working/building/REAL300024450502 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/374 `/scratch/stefan/7786230/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450502/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450502 none CC[NH+](CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 196, 201, 201, 201, 115, 115, 115, 78, 78, 78, 78, 78, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 115, 78, 78, 78, 78, 78, 78, 78, 30, 30, 1, 78, 78, 78, 78] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 794 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450502 none CC[NH+](CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 32, 18, 32, 32, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 78, 78, 78, 78, 78, 1, 1, 33, 33, 33, 33, 33, 35, 35, 35, 35, 35, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 78, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 287 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450502 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450502 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450502/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450502 Building REAL300024450503 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450503' /scratch/stefan/7786230/working/building/REAL300024450503 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450503 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450503/0 /scratch/stefan/7786230/working/building/REAL300024450503 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/375 `/scratch/stefan/7786230/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450503/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450503 none CCC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6] 6 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44]) total number of confs: 12 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450503 none CCC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 1, 2, 2, 2] 6 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450503 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450503 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450503/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450503 Building REAL300024450504 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450504' /scratch/stefan/7786230/working/building/REAL300024450504 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450504 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450504/0 /scratch/stefan/7786230/working/building/REAL300024450504 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/376 `/scratch/stefan/7786230/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450504/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450504 none CC1C(NC(=O)CCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 54, 54, 76, 76, 76, 179, 196, 201, 54, 54, 54, 54, 39, 54, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 76, 179, 179, 201, 201, 201, 201, 54, 54, 54, 54, 54, 54, 39, 39, 1] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 880 number of broken/clashed sets: 46 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450504 none CC1C(NC(=O)CCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 27, 43, 1, 1, 1, 1, 1, 3, 3, 9, 14, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 4, 20, 20, 33, 33, 40, 40, 1, 1, 1, 1, 1, 1, 9, 9, 54] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 300 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450504 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450504 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450504/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450504 Building REAL300024450505 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450505' /scratch/stefan/7786230/working/building/REAL300024450505 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450505 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450505/0 /scratch/stefan/7786230/working/building/REAL300024450505 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/377 `/scratch/stefan/7786230/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)(F)F) `REAL300024450505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450505/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450505 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 114, 114, 114, 108, 108, 108, 108, 108, 106, 53, 106, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 114, 108, 108, 108, 108, 108, 108, 108, 53, 53, 1, 108, 108, 108, 108] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44]) total number of confs: 795 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450505 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 32, 108, 108, 108, 108, 108, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 108, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450505 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450505 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450505/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450505 Building REAL300024450506 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450506' /scratch/stefan/7786230/working/building/REAL300024450506 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450506 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450506/0 /scratch/stefan/7786230/working/building/REAL300024450506 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/378 `/scratch/stefan/7786230/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450506/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450506 none CC1=COC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 32, 102, 102, 102, 102, 102, 1, 1, 13, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 102, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 193 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: REAL300024450506 none CC1=COC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 116, 116, 116, 102, 102, 102, 102, 102, 101, 47, 101, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 116, 102, 102, 102, 102, 102, 102, 102, 47, 47, 1, 102, 102, 102, 102] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 514 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450506 none CC1=COC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 13, 13, 13, 13, 13, 22, 22, 62, 108, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 1, 10, 13, 13, 13, 13, 13, 13, 13, 62, 62, 201, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 472 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450506 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450506 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450506/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450506 Building REAL300024450507 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450507' /scratch/stefan/7786230/working/building/REAL300024450507 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450507 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450507/0 /scratch/stefan/7786230/working/building/REAL300024450507 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/379 `/scratch/stefan/7786230/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450507/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450507 none C[C@H]1C[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 3, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 73, 73, 73, 73, 73, 1, 1, 16, 16, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 73, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 23 ./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: REAL300024450507 none C[C@H]1C[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 201, 78, 78, 73, 73, 73, 73, 73, 72, 35, 72, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 78, 73, 73, 73, 73, 73, 73, 73, 35, 35, 1, 73, 73, 73, 73] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 605 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450507 none C[C@H]1C[C@@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 16, 16, 16, 16, 16, 25, 25, 60, 104, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 1, 12, 16, 16, 16, 16, 16, 16, 16, 60, 60, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 457 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450507 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450507 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450507/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450507 Building REAL300024450508 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450508' /scratch/stefan/7786230/working/building/REAL300024450508 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450508 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450508/0 /scratch/stefan/7786230/working/building/REAL300024450508 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/380 `/scratch/stefan/7786230/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450508/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450508 none CC1C(NC(=O)C2(C)C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 44, 101, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 44, 44, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 426 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: REAL300024450508 none CC1C(NC(=O)C2(C)C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 103, 103, 103, 106, 106, 106, 201, 201, 201, 201, 201, 103, 103, 103, 101, 46, 101, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 103, 46, 46, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 629 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450508 none CC1C(NC(=O)C2(C)C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 12, 33, 103, 103, 103, 103, 103, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 103] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450508 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450508 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450508/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450508 Building REAL300024450509 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450509' /scratch/stefan/7786230/working/building/REAL300024450509 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450509 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450509/0 /scratch/stefan/7786230/working/building/REAL300024450509 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/381 `/scratch/stefan/7786230/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450509/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450509 none CC1C(NC(=O)[C@@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 51, 102, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 51, 51, 201] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 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: 448 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: REAL300024450509 none CC1C(NC(=O)[C@@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [133, 133, 133, 133, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 129, 57, 129, 12, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 150, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 57, 57, 1] 201 rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 664 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450509 none CC1C(NC(=O)[C@@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 39, 133, 133, 133, 133, 133, 2, 2, 2, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 133] 201 rigid atoms, others: [0, 1, 2, 3, 32, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 46, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450509 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450509 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450509/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450509 Building REAL300024450510 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450510' /scratch/stefan/7786230/working/building/REAL300024450510 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450510 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450510/0 /scratch/stefan/7786230/working/building/REAL300024450510 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/382 `/scratch/stefan/7786230/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450510/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450510 none CC1C(NC(=O)C2=NN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 30, 48, 90, 90, 90, 90, 90, 8, 8, 8, 8, 8, 7, 2, 2, 2, 8, 8, 8, 8, 8, 8, 30, 30, 90] 90 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 18 ./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: REAL300024450510 none CC1C(NC(=O)C2=NN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 78, 78, 78, 90, 90, 90, 90, 90, 77, 77, 77, 73, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 78, 90, 90, 90, 77, 77, 77, 77, 77, 77, 39, 39, 1] 90 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450510 none CC1C(NC(=O)C2=NN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 14, 28, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 14, 77] 90 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450510 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450510 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450510/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450510 Building REAL300024450511 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450511' /scratch/stefan/7786230/working/building/REAL300024450511 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450511 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450511/0 /scratch/stefan/7786230/working/building/REAL300024450511 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/383 `/scratch/stefan/7786230/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450511/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450511 none CC1C(NC(=O)C2CCCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 32, 85, 173, 173, 173, 173, 173, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 32, 32, 173] 173 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 348 number of broken/clashed sets: 42 ./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: REAL300024450511 none CC1C(NC(=O)C2CCCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 166, 166, 166, 173, 173, 173, 173, 173, 173, 165, 165, 165, 158, 67, 158, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 166, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 173, 165, 165, 165, 165, 165, 165, 67, 67, 1] 173 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 524 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450511 none CC1C(NC(=O)C2CCCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 17, 56, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 17, 165] 173 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 280 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450511 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450511 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450511/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450511 Building REAL300024450512 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450512' /scratch/stefan/7786230/working/building/REAL300024450512 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450512 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450512/0 /scratch/stefan/7786230/working/building/REAL300024450512 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/384 `/scratch/stefan/7786230/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450512/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450512 none CC1CCC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 56, 56, 56, 56, 56, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 1, 2, 2, 2, 32, 32] 201 rigid atoms, others: [45, 43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52, 53, 54]) total number of confs: 208 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: REAL300024450512 none CC1CCC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 193, 64, 64, 64, 56, 56, 56, 56, 56, 50, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 64, 56, 56, 56, 56, 56, 56, 56, 25, 25, 1, 56, 56, 56, 56, 201, 201] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 743 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450512 none CC1CCC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 24, 24, 24, 32, 32, 32, 32, 32, 51, 51, 90, 131, 201, 201, 201, 201, 201, 32, 32, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 24, 32, 32, 32, 32, 32, 32, 32, 90, 90, 201, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 35, 53, 54, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 564 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450512 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450512 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450512/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450512 Building REAL300024450513 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450513' /scratch/stefan/7786230/working/building/REAL300024450513 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450513 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450513/0 /scratch/stefan/7786230/working/building/REAL300024450513 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/385 `/scratch/stefan/7786230/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)N=C1) `REAL300024450513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450513/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450513 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)N=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 29, 89, 89, 89, 89, 89, 1, 1, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 89, 1, 2, 2, 2, 14, 14, 14, 14] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 29 ./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: REAL300024450513 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)N=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 98, 98, 98, 89, 89, 89, 89, 89, 87, 42, 87, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 98, 89, 89, 89, 89, 89, 89, 89, 42, 42, 1, 89, 89, 89, 89, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 471 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450513 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)N=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 14, 14, 14, 14, 14, 21, 21, 56, 96, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 14, 56, 56, 201, 14, 14, 14, 14, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 456 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450513 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450513 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450513/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450513 Building REAL300024450514 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450514' /scratch/stefan/7786230/working/building/REAL300024450514 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450514 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450514/0 /scratch/stefan/7786230/working/building/REAL300024450514 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/386 `/scratch/stefan/7786230/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450514/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450514 none CC(C)C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 6, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6] 8 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 19 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450514 none CC(C)C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 5, 6, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 1, 2, 2, 2] 8 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 48 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450514 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450514 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450514/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450514 Building REAL300024450515 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450515' /scratch/stefan/7786230/working/building/REAL300024450515 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450515 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450515/0 /scratch/stefan/7786230/working/building/REAL300024450515 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/387 `/scratch/stefan/7786230/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450515/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450515 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 29, 79, 79, 79, 79, 79, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 79, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 29 ./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: REAL300024450515 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 198, 92, 92, 92, 79, 79, 79, 79, 79, 73, 27, 73, 12, 1, 1, 1, 1, 1, 1, 1, 79, 79, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 92, 79, 79, 79, 79, 79, 79, 79, 27, 27, 1, 79, 79, 79, 79, 198, 198, 198, 198, 198, 198] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 610 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450515 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 18, 18, 63, 117, 198, 198, 198, 198, 198, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 10, 10, 10, 10, 10, 10, 10, 63, 63, 198, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 49, 50, 51, 52, 53, 54, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 488 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450515 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450515 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450515/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450515 Building REAL300024450516 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450516' /scratch/stefan/7786230/working/building/REAL300024450516 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450516 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450516/0 /scratch/stefan/7786230/working/building/REAL300024450516 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/388 `/scratch/stefan/7786230/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450516/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450516 none C=CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 141, 200, 141, 141, 118, 118, 118, 118, 118, 105, 30, 105, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 141, 118, 118, 118, 118, 118, 118, 118, 30, 30, 1, 118, 118, 118, 118] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 740 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450516 none C=CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 11, 19, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 32, 118, 118, 118, 118, 118, 1, 1, 28, 28, 28, 19, 19, 19, 19, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 118, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450516 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450516 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450516/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450516 Building REAL300024450517 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450517' /scratch/stefan/7786230/working/building/REAL300024450517 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450517 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450517/0 /scratch/stefan/7786230/working/building/REAL300024450517 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/389 `/scratch/stefan/7786230/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450517/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450517 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 33, 87, 87, 87, 87, 87, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 87, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 29 ./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: REAL300024450517 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 88, 88, 88, 87, 87, 87, 87, 87, 85, 44, 85, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 88, 87, 87, 87, 87, 87, 87, 87, 44, 44, 1, 87, 87, 87, 87, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 601 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450517 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 9, 9, 9, 9, 9, 14, 14, 47, 99, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 3, 3, 3, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 47, 47, 201, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 46, 47, 48, 49, 50, 51, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 421 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450517 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450517 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450517/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450517 Building REAL300024450518 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450518' /scratch/stefan/7786230/working/building/REAL300024450518 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450518 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450518/0 /scratch/stefan/7786230/working/building/REAL300024450518 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/390 `/scratch/stefan/7786230/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3(CCC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450518/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450518 none CC1C(NC(=O)C2CC3(CCC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 65, 109, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 65, 65, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 472 number of broken/clashed sets: 39 ./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: REAL300024450518 none CC1C(NC(=O)C2CC3(CCC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 78, 78, 78, 201, 201, 201, 201, 201, 201, 77, 77, 77, 75, 42, 75, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 77, 42, 42, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 617 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450518 none CC1C(NC(=O)C2CC3(CCC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 11, 23, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 11, 11, 77] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450518 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450518 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450518/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450518 Building REAL300024450519 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450519' /scratch/stefan/7786230/working/building/REAL300024450519 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450519 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450519/0 /scratch/stefan/7786230/working/building/REAL300024450519 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/391 `/scratch/stefan/7786230/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450519/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450519 none CC#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 143, 129, 36, 36, 36, 29, 29, 29, 29, 29, 29, 20, 29, 12, 1, 1, 1, 1, 1, 1, 1, 29, 29, 201, 201, 201, 188, 188, 174, 174, 129, 129, 36, 29, 29, 29, 29, 29, 29, 29, 20, 20, 1, 29, 29, 29, 29] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 1009 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450519 none CC#CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 19, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 10, 29, 29, 29, 29, 29, 1, 1, 45, 45, 45, 41, 42, 24, 24, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450519 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450519 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450519/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450519 Building REAL300024450520 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450520' /scratch/stefan/7786230/working/building/REAL300024450520 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450520 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450520/0 /scratch/stefan/7786230/working/building/REAL300024450520 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/392 `/scratch/stefan/7786230/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450520/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450520 none CC1C(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 26, 26, 66, 107, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 13, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 66, 66, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 38] set([0, 1, 2, 3, 5, 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]) total number of confs: 469 number of broken/clashed sets: 25 ./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: REAL300024450520 none CC1C(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 86, 45, 86, 12, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 91, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 45, 45, 1] 201 rigid atoms, others: [47, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 614 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450520 none CC1C(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 12, 27, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 12, 12, 89] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 40, 41, 42, 39, 44, 15, 16, 17, 18, 19, 43] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450520 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450520 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450520/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450520 Building REAL300024450521 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450521' /scratch/stefan/7786230/working/building/REAL300024450521 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450521 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450521/0 /scratch/stefan/7786230/working/building/REAL300024450521 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/393 `/scratch/stefan/7786230/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450521/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450521 none CC1C(NC(=O)CCCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 31, 31, 7, 31, 3, 3, 1, 1, 1, 1, 34, 34, 34, 34, 34, 35, 35, 89, 128, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 31, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 89, 89, 201] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 563 number of broken/clashed sets: 41 ./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: REAL300024450521 none CC1C(NC(=O)CCCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 41, 41, 41, 153, 152, 183, 201, 201, 34, 34, 34, 33, 21, 33, 13, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 41, 153, 153, 183, 183, 183, 183, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 34, 21, 21, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1003 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450521 none CC1C(NC(=O)CCCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 17, 21, 34, 34, 1, 1, 1, 1, 1, 3, 3, 6, 10, 34, 34, 34, 34, 34, 2, 2, 2, 1, 1, 3, 13, 13, 21, 21, 21, 21, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 6, 6, 34] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450521 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450521 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450521/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450521 Building REAL300024450522 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450522' /scratch/stefan/7786230/working/building/REAL300024450522 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450522 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450522/0 /scratch/stefan/7786230/working/building/REAL300024450522 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/394 `/scratch/stefan/7786230/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCN(C)C2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450522/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450522 none CC1C(NC(=O)C2CCN(C)C2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 25, 25, 77, 117, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 77, 77, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 507 number of broken/clashed sets: 27 ./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: REAL300024450522 none CC1C(NC(=O)C2CCN(C)C2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [112, 112, 112, 112, 128, 128, 128, 201, 201, 201, 201, 201, 201, 112, 112, 112, 110, 39, 110, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 128, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 112, 112, 112, 39, 39, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 622 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450522 none CC1C(NC(=O)C2CCN(C)C2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 11, 27, 112, 112, 112, 112, 112, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 11, 11, 112] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450522 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450522 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450522/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450522 Building REAL300024450523 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450523' /scratch/stefan/7786230/working/building/REAL300024450523 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450523 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450523/0 /scratch/stefan/7786230/working/building/REAL300024450523 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/395 `/scratch/stefan/7786230/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450523/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450523 none CCCC(OCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 154, 85, 154, 161, 161, 85, 85, 69, 69, 69, 69, 69, 67, 37, 67, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 154, 161, 161, 161, 161, 161, 85, 69, 69, 69, 69, 69, 69, 69, 37, 37, 1, 69, 69, 69, 69] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 958 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450523 none CCCC(OCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 19, 11, 3, 11, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 69, 69, 69, 69, 69, 1, 1, 22, 22, 22, 22, 22, 21, 21, 11, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450523 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450523 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450523/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450523 Building REAL300024450524 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450524' /scratch/stefan/7786230/working/building/REAL300024450524 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450524 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450524/0 /scratch/stefan/7786230/working/building/REAL300024450524 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/396 `/scratch/stefan/7786230/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450524/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450524 none CC1C(NC(=O)C2CCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 47, 110, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 47, 47, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 438 number of broken/clashed sets: 25 ./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: REAL300024450524 none CC1C(NC(=O)C2CCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [140, 140, 140, 140, 148, 148, 148, 201, 201, 201, 201, 201, 140, 140, 140, 137, 58, 137, 13, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 140, 58, 58, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 657 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450524 none CC1C(NC(=O)C2CCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 13, 40, 140, 140, 140, 140, 140, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 13, 13, 140] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450524 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450524 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450524/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450524 Building REAL300024450525 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450525' /scratch/stefan/7786230/working/building/REAL300024450525 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450525 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450525/0 /scratch/stefan/7786230/working/building/REAL300024450525 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/397 `/scratch/stefan/7786230/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450525/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450525 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 77, 77, 77, 77, 77, 1, 1, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 77, 1, 2, 2, 2, 10] 93 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 166 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: REAL300024450525 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 80, 80, 80, 77, 77, 77, 77, 77, 74, 38, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 93, 93, 93, 93, 93, 80, 77, 77, 77, 77, 77, 77, 77, 38, 38, 1, 77, 77, 77, 77, 93] 93 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450525 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 12, 12, 35, 56, 93, 93, 93, 93, 93, 10, 10, 1, 2, 2, 2, 1, 5, 10, 10, 10, 10, 10, 10, 10, 35, 35, 93, 10, 10, 10, 10, 1] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450525 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450525 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450525/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450525 Building REAL300024450526 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450526' /scratch/stefan/7786230/working/building/REAL300024450526 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450526 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450526/0 /scratch/stefan/7786230/working/building/REAL300024450526 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/398 `/scratch/stefan/7786230/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CSC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450526/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450526 none CC1C(NC(=O)C2=CSC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 23, 23, 63, 109, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 11, 1, 1, 16, 16, 16, 16, 16, 16, 63, 63, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 478 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: REAL300024450526 none CC1C(NC(=O)C2=CSC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 110, 110, 110, 201, 201, 201, 201, 201, 80, 80, 80, 79, 44, 79, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 110, 201, 201, 80, 80, 80, 80, 80, 80, 44, 44, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 523 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450526 none CC1C(NC(=O)C2=CSC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 11, 24, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 3, 16, 16, 1, 1, 1, 1, 1, 1, 11, 11, 80] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450526 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450526 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450526/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450526 Building REAL300024450527 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450527' /scratch/stefan/7786230/working/building/REAL300024450527 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450527 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450527/0 /scratch/stefan/7786230/working/building/REAL300024450527 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/399 `/scratch/stefan/7786230/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450527/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450527 none C=CC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 201, 201, 84, 84, 84, 64, 64, 64, 64, 64, 61, 28, 61, 12, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 84, 64, 64, 64, 64, 64, 64, 64, 28, 28, 1, 64, 64, 64, 64] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 849 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450527 none C=CC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 26, 15, 26, 28, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 64, 64, 64, 64, 64, 1, 1, 31, 31, 31, 26, 28, 28, 28, 28, 28, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 256 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450527 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450527 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450527/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450527 Building REAL300024450528 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450528' /scratch/stefan/7786230/working/building/REAL300024450528 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450528 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450528/0 /scratch/stefan/7786230/working/building/REAL300024450528 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/400 `/scratch/stefan/7786230/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450528/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450528 none CC1C(NC(=O)C(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 1, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [6, 38, 39, 40, 9, 10, 11, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 23 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: REAL300024450528 none CC1C(NC(=O)C(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 1] 5 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 17 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450528 none CC1C(NC(=O)C(C)(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2] 5 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450528 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450528 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450528/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450528 Building REAL300024450529 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450529' /scratch/stefan/7786230/working/building/REAL300024450529 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450529 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450529/0 /scratch/stefan/7786230/working/building/REAL300024450529 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/401 `/scratch/stefan/7786230/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450529/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450529 none CC1C(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 38, 38, 93, 127, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 93, 93, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 554 number of broken/clashed sets: 35 ./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: REAL300024450529 none CC1C(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 96, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 59, 37, 59, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 96, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 37, 37, 1] 201 rigid atoms, others: [49, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 652 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450529 none CC1C(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 13, 21, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 6, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 13, 13, 62] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450529 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450529 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450529/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450529 Building REAL300024450530 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450530' /scratch/stefan/7786230/working/building/REAL300024450530 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450530 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450530/0 /scratch/stefan/7786230/working/building/REAL300024450530 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/402 `/scratch/stefan/7786230/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450530/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450530 none CC1C(NC(=O)CC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 64, 109, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 13, 5, 5, 1, 1, 25, 25, 25, 25, 25, 25, 64, 64, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 55 ./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: REAL300024450530 none CC1C(NC(=O)CC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 55, 55, 55, 117, 201, 201, 201, 201, 41, 41, 41, 41, 38, 41, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 55, 117, 117, 201, 201, 41, 41, 41, 41, 41, 41, 38, 38, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 640 number of broken/clashed sets: 55 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450530 none CC1C(NC(=O)CC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 6, 10, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 3, 9, 9, 25, 25, 1, 1, 1, 1, 1, 1, 6, 6, 41] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450530 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450530 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450530/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450530 Building REAL300024450531 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450531' /scratch/stefan/7786230/working/building/REAL300024450531 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450531 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450531/0 /scratch/stefan/7786230/working/building/REAL300024450531 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/403 `/scratch/stefan/7786230/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450531/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450531 none CC1C(NC(=O)[C@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 50, 111, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 201] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 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: 431 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: REAL300024450531 none CC1C(NC(=O)[C@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [140, 140, 140, 140, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 137, 57, 137, 12, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 150, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 140, 57, 57, 1] 201 rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 666 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450531 none CC1C(NC(=O)[C@H]2CCC(=O)N2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 42, 140, 140, 140, 140, 140, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 140] 201 rigid atoms, others: [0, 1, 2, 3, 32, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 46, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450531 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450531 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450531/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450531 Building REAL300024450532 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450532' /scratch/stefan/7786230/working/building/REAL300024450532 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450532 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450532/0 /scratch/stefan/7786230/working/building/REAL300024450532 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/404 `/scratch/stefan/7786230/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450532/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450532 none CC1C(NC(=O)CC2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 30, 30, 6, 30, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 55, 55, 88, 132, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 30, 6, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 39, 39, 39, 39, 39, 39, 88, 88, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 548 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: REAL300024450532 none CC1C(NC(=O)CC2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 72, 72, 72, 144, 201, 201, 201, 201, 201, 58, 58, 58, 56, 27, 56, 12, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 72, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 27, 27, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 806 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450532 none CC1C(NC(=O)CC2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 18, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 9, 16, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 18, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 9, 9, 58] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 228 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450532 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450532 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450532/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450532 Building REAL300024450533 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450533' /scratch/stefan/7786230/working/building/REAL300024450533 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450533 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450533/0 /scratch/stefan/7786230/working/building/REAL300024450533 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/405 `/scratch/stefan/7786230/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(F)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450533/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450533 none CC1C(NC(=O)C2(F)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 60, 120, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 60, 60, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 472 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: REAL300024450533 none CC1C(NC(=O)C2(F)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [123, 123, 123, 123, 141, 141, 141, 201, 201, 201, 201, 201, 123, 123, 123, 123, 53, 123, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 141, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 123, 53, 53, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 664 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450533 none CC1C(NC(=O)C2(F)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 34, 123, 123, 123, 123, 123, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 123] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 221 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450533 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450533 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450533/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450533 Building REAL300024450534 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450534' /scratch/stefan/7786230/working/building/REAL300024450534 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450534 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450534/0 /scratch/stefan/7786230/working/building/REAL300024450534 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/406 `/scratch/stefan/7786230/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1C) `REAL300024450534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450534/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450534 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 29, 80, 80, 80, 80, 80, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 80, 1, 2, 2, 2, 13, 13, 13] 155 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 166 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: REAL300024450534 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 83, 83, 83, 80, 80, 80, 80, 80, 76, 42, 76, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 155, 155, 155, 155, 155, 155, 83, 80, 80, 80, 80, 80, 80, 80, 42, 42, 1, 80, 80, 80, 80, 155, 155, 155] 155 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 390 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450534 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 13, 18, 18, 56, 97, 155, 155, 155, 155, 155, 13, 13, 1, 1, 2, 2, 2, 1, 9, 13, 13, 13, 13, 13, 13, 13, 56, 56, 155, 13, 13, 13, 13, 2, 2, 2] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 391 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450534 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450534 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450534/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450534 Building REAL300024450535 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450535' /scratch/stefan/7786230/working/building/REAL300024450535 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450535 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450535/0 /scratch/stefan/7786230/working/building/REAL300024450535 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/407 `/scratch/stefan/7786230/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450535/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450535 none CC1C(NC(=O)CCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 99, 99, 99, 201, 201, 201, 201, 201, 70, 70, 70, 68, 40, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 40, 40, 1] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 53] 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, 48, 49, 50, 51, 52]) total number of confs: 797 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450535 none CC1C(NC(=O)CCC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 21, 21, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 11, 19, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 6, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 11, 11, 70] 201 rigid atoms, others: [0, 1, 2, 3, 16, 45, 12, 13, 46, 15, 48, 49, 50, 14, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450535 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450535 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450535/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450535 Building REAL300024450536 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450536' /scratch/stefan/7786230/working/building/REAL300024450536 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450536 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450536/0 /scratch/stefan/7786230/working/building/REAL300024450536 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/408 `/scratch/stefan/7786230/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450536/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450536 none CC1C(NC(=O)C2=CC=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 54, 108, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 54, 54, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 442 number of broken/clashed sets: 20 ./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: REAL300024450536 none CC1C(NC(=O)C2=CC=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 164, 69, 164, 13, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 201, 201, 201, 201, 171, 171, 171, 171, 171, 171, 69, 69, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 620 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450536 none CC1C(NC(=O)C2=CC=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 4, 4, 15, 47, 171, 171, 171, 171, 171, 2, 2, 2, 1, 1, 6, 10, 10, 10, 1, 1, 1, 1, 1, 1, 15, 15, 171] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 280 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450536 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450536 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450536/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450536 Building REAL300024450537 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450537' /scratch/stefan/7786230/working/building/REAL300024450537 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450537 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450537/0 /scratch/stefan/7786230/working/building/REAL300024450537 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/409 `/scratch/stefan/7786230/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CC=N1) `REAL300024450537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450537/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450537 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 56, 56, 56, 56, 56, 1, 1, 10, 10, 4, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 1, 2, 2, 2, 10, 10] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 24 ./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: REAL300024450537 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 57, 57, 56, 56, 56, 56, 56, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 57, 201, 201, 201, 201, 57, 56, 56, 56, 56, 56, 56, 56, 30, 30, 1, 56, 56, 56, 56, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47]) total number of confs: 626 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450537 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 10, 10, 10, 10, 10, 14, 14, 48, 87, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 1, 5, 10, 10, 10, 10, 10, 10, 10, 48, 48, 201, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 47, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 429 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450537 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450537 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450537/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450537 Building REAL300024450538 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450538' /scratch/stefan/7786230/working/building/REAL300024450538 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450538 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450538/0 /scratch/stefan/7786230/working/building/REAL300024450538 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/410 `/scratch/stefan/7786230/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450538/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450538 none CC1C(NC(=O)CC2=CC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 25, 25, 4, 25, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 46, 46, 82, 124, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 25, 4, 4, 1, 1, 1, 30, 30, 30, 30, 30, 30, 82, 82, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 538 number of broken/clashed sets: 9 ./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: REAL300024450538 none CC1C(NC(=O)CC2=CC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 79, 79, 79, 151, 201, 201, 201, 201, 72, 72, 72, 69, 27, 69, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 79, 151, 151, 201, 201, 201, 72, 72, 72, 72, 72, 72, 27, 27, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 656 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450538 none CC1C(NC(=O)CC2=CC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 18, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 3, 15, 15, 30, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 72] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450538 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450538 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450538/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450538 Building REAL300024450539 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450539' /scratch/stefan/7786230/working/building/REAL300024450539 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450539 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450539/0 /scratch/stefan/7786230/working/building/REAL300024450539 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/411 `/scratch/stefan/7786230/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450539/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450539 none CC1C(NC(=O)C2=NC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 31, 45, 81, 81, 81, 81, 81, 10, 10, 10, 10, 10, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 31, 31, 81] 81 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 200 number of broken/clashed sets: 14 ./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: REAL300024450539 none CC1C(NC(=O)C2=NC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 163, 69, 163, 13, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 69, 69, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 630 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450539 none CC1C(NC(=O)C2=NC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1, 3, 3, 14, 47, 167, 167, 167, 167, 167, 2, 2, 2, 1, 1, 6, 11, 6, 11, 1, 1, 1, 1, 1, 1, 14, 14, 167] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 286 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450539 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450539 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450539/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450539 Building REAL300024450540 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450540' /scratch/stefan/7786230/working/building/REAL300024450540 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450540 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450540/0 /scratch/stefan/7786230/working/building/REAL300024450540 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/412 `/scratch/stefan/7786230/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450540/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450540 none CCC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 149, 201, 137, 45, 45, 45, 40, 40, 40, 40, 40, 36, 23, 36, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 137, 137, 45, 40, 40, 40, 40, 40, 40, 40, 23, 23, 1, 40, 40, 40, 40] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 986 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450540 none CCC(C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 41, 18, 41, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 40, 40, 40, 40, 40, 1, 1, 45, 45, 45, 45, 45, 41, 41, 41, 41, 20, 20, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 284 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450540 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450540 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450540/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450540 Building REAL300024450541 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450541' /scratch/stefan/7786230/working/building/REAL300024450541 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450541 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450541/0 /scratch/stefan/7786230/working/building/REAL300024450541 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/413 `/scratch/stefan/7786230/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450541/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450541 none CC1C(NC(=O)C2=CC=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 30, 42, 73, 73, 73, 73, 73, 9, 9, 9, 9, 9, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 30, 30, 73] 73 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 178 number of broken/clashed sets: 14 ./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: REAL300024450541 none CC1C(NC(=O)C2=CC=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 70, 70, 70, 73, 73, 73, 73, 73, 65, 65, 65, 64, 40, 64, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 70, 73, 73, 73, 65, 65, 65, 65, 65, 65, 40, 40, 1] 73 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 243 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450541 none CC1C(NC(=O)C2=CC=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 14, 27, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 4, 9, 9, 9, 1, 1, 1, 1, 1, 1, 14, 14, 65] 73 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450541 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450541 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450541/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450541 Building REAL300024450542 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450542' /scratch/stefan/7786230/working/building/REAL300024450542 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450542 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450542/0 /scratch/stefan/7786230/working/building/REAL300024450542 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/414 `/scratch/stefan/7786230/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C(C)O1) `REAL300024450542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450542/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450542 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 29, 67, 67, 67, 67, 67, 1, 1, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 67, 1, 2, 2, 2, 7, 7, 7] 88 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 152 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: REAL300024450542 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 88, 88, 83, 83, 83, 67, 67, 67, 67, 67, 64, 35, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 88, 88, 88, 88, 88, 88, 83, 67, 67, 67, 67, 67, 67, 67, 35, 35, 1, 67, 67, 67, 67, 88, 88, 88] 88 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 288 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450542 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 7, 7, 7, 10, 10, 34, 53, 88, 88, 88, 88, 88, 7, 7, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 34, 34, 88, 7, 7, 7, 7, 1, 1, 1] 88 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 47, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 231 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450542 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450542 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450542/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450542 Building REAL300024450543 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450543' /scratch/stefan/7786230/working/building/REAL300024450543 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450543 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450543/0 /scratch/stefan/7786230/working/building/REAL300024450543 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/415 `/scratch/stefan/7786230/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCN2C=NN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450543/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450543 none CC1C(NC(=O)CCN2C=NN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 40, 40, 13, 40, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 57, 57, 77, 91, 116, 116, 116, 116, 116, 42, 42, 42, 42, 42, 40, 13, 13, 6, 6, 1, 42, 42, 42, 42, 42, 42, 77, 77, 116] 116 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 369 number of broken/clashed sets: 9 ./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: REAL300024450543 none CC1C(NC(=O)CCN2C=NN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 36, 36, 36, 90, 99, 116, 116, 116, 116, 32, 32, 32, 32, 19, 32, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 36, 90, 90, 99, 99, 116, 32, 32, 32, 32, 32, 32, 19, 19, 1] 116 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 424 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450543 none CC1C(NC(=O)CCN2C=NN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 22, 42, 42, 42, 42, 1, 1, 1, 1, 1, 3, 3, 9, 13, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 3, 12, 12, 22, 22, 42, 1, 1, 1, 1, 1, 1, 9, 9, 32] 116 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450543 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450543 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450543/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450543 Building REAL300024450544 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450544' /scratch/stefan/7786230/working/building/REAL300024450544 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450544 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450544/0 /scratch/stefan/7786230/working/building/REAL300024450544 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/416 `/scratch/stefan/7786230/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=CC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450544/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450544 none CC1C(NC(=O)C2=NC=CC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 20, 20, 66, 94, 147, 147, 147, 147, 147, 15, 15, 15, 15, 15, 10, 1, 1, 1, 15, 15, 15, 15, 15, 15, 66, 66, 147] 147 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 383 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: REAL300024450544 none CC1C(NC(=O)C2=NC=CC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 110, 110, 110, 147, 147, 147, 147, 147, 147, 90, 90, 90, 82, 41, 82, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 110, 147, 147, 147, 90, 90, 90, 90, 90, 90, 41, 41, 1] 147 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 419 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450544 none CC1C(NC(=O)C2=NC=CC=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 16, 35, 90, 90, 90, 90, 90, 2, 2, 2, 1, 1, 4, 15, 15, 15, 1, 1, 1, 1, 1, 1, 16, 16, 90] 147 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450544 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450544 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450544/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450544 Building REAL300024450545 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450545' /scratch/stefan/7786230/working/building/REAL300024450545 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450545 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450545/0 /scratch/stefan/7786230/working/building/REAL300024450545 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/417 `/scratch/stefan/7786230/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450545/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450545 none CC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 62, 175, 175, 175, 175, 175, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 175, 1, 2, 2, 2] 199 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 298 number of broken/clashed sets: 62 ./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: REAL300024450545 none CC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [199, 199, 199, 199, 199, 177, 177, 177, 175, 175, 175, 175, 175, 163, 66, 163, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 199, 199, 199, 199, 199, 199, 199, 199, 199, 177, 175, 175, 175, 175, 175, 175, 175, 66, 66, 1, 175, 175, 175, 175] 199 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 62 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450545 none CC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 11, 11, 43, 106, 199, 199, 199, 199, 199, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 43, 43, 199, 6, 6, 6, 6] 199 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 401 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450545 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450545 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450545/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450545 Building REAL300024450546 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450546' /scratch/stefan/7786230/working/building/REAL300024450546 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450546 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450546/0 /scratch/stefan/7786230/working/building/REAL300024450546 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/418 `/scratch/stefan/7786230/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450546/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450546 none CC1C(NC(=O)C2(C)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 44, 96, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 44, 44, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 416 number of broken/clashed sets: 27 ./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: REAL300024450546 none CC1C(NC(=O)C2(C)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 104, 104, 113, 113, 113, 201, 201, 201, 201, 201, 104, 104, 104, 100, 49, 100, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 104, 49, 49, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 615 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450546 none CC1C(NC(=O)C2(C)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 13, 36, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 13, 13, 104] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450546 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450546 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450546/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450546 Building REAL300024450547 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450547' /scratch/stefan/7786230/working/building/REAL300024450547 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450547 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450547/0 /scratch/stefan/7786230/working/building/REAL300024450547 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/419 `/scratch/stefan/7786230/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450547/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450547 none CCC(CC)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2] 2 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 3 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450547 none CCC(CC)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2] 2 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450547 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450547 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450547/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450547 Building REAL300024450548 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450548' /scratch/stefan/7786230/working/building/REAL300024450548 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450548 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450548/0 /scratch/stefan/7786230/working/building/REAL300024450548 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/420 `/scratch/stefan/7786230/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1) `REAL300024450548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450548/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450548 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 24, 72, 72, 72, 72, 72, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 72, 1, 2, 2, 2, 18, 18, 18, 18] 193 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 44 ./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: REAL300024450548 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [193, 193, 193, 73, 73, 73, 72, 72, 72, 72, 72, 67, 41, 67, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 73, 72, 72, 72, 72, 72, 72, 72, 41, 41, 1, 72, 72, 72, 72, 193, 193, 193, 193] 193 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 582 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450548 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 18, 18, 18, 25, 25, 77, 115, 193, 193, 193, 193, 193, 18, 18, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 13, 18, 18, 18, 18, 18, 18, 18, 77, 77, 193, 18, 18, 18, 18, 1, 1, 1, 1] 193 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 51, 52, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 506 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450548 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450548 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450548/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450548 Building REAL300024450549 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450549' /scratch/stefan/7786230/working/building/REAL300024450549 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450549 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450549/0 /scratch/stefan/7786230/working/building/REAL300024450549 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/421 `/scratch/stefan/7786230/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450549/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450549 none CCCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 177, 109, 177, 177, 167, 109, 109, 92, 92, 92, 92, 92, 80, 30, 80, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 178, 178, 178, 178, 178, 109, 92, 92, 92, 92, 92, 92, 92, 30, 30, 1, 92, 92, 92, 92] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 966 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450549 none CCCC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 3, 8, 8, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 32, 92, 92, 92, 92, 92, 1, 1, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 92, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 234 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450549 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450549 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450549/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450549 Building REAL300024450550 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450550' /scratch/stefan/7786230/working/building/REAL300024450550 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450550 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450550/0 /scratch/stefan/7786230/working/building/REAL300024450550 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/422 `/scratch/stefan/7786230/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450550/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450550 none CCC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 194, 201, 201, 71, 71, 71, 55, 55, 55, 55, 55, 52, 22, 52, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 71, 55, 55, 55, 55, 55, 55, 55, 22, 22, 1, 55, 55, 55, 55] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 780 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450550 none CCC(CC)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 30, 16, 29, 32, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 55, 55, 55, 55, 55, 1, 1, 33, 33, 33, 33, 33, 30, 32, 31, 32, 32, 32, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 255 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450550 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450550 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450550/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450550 Building REAL300024450551 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450551' /scratch/stefan/7786230/working/building/REAL300024450551 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450551 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450551/0 /scratch/stefan/7786230/working/building/REAL300024450551 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/423 `/scratch/stefan/7786230/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450551/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450551 none CCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 195, 201, 115, 195, 115, 115, 92, 92, 92, 92, 92, 84, 28, 84, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 115, 92, 92, 92, 92, 92, 92, 92, 28, 28, 1, 92, 92, 92, 92] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 778 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450551 none CCC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 20, 12, 21, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 27, 92, 92, 92, 92, 92, 1, 1, 25, 25, 25, 25, 24, 21, 21, 21, 21, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 92, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 262 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450551 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450551 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450551/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450551 Building REAL300024450552 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450552' /scratch/stefan/7786230/working/building/REAL300024450552 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450552 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450552/0 /scratch/stefan/7786230/working/building/REAL300024450552 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/424 `/scratch/stefan/7786230/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450552/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450552 none CCCC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 195, 171, 91, 171, 173, 91, 91, 78, 78, 78, 78, 78, 72, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 201, 201, 201, 195, 195, 171, 182, 182, 182, 182, 182, 91, 78, 78, 78, 78, 78, 78, 78, 28, 28, 1, 78, 78, 78, 78] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 971 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450552 none CCCC(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 23, 11, 3, 11, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 78, 78, 78, 78, 78, 1, 1, 25, 25, 25, 25, 25, 23, 23, 11, 15, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 78, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 279 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450552 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450552 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450552/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450552 Building REAL300024450553 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450553' /scratch/stefan/7786230/working/building/REAL300024450553 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450553 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450553/0 /scratch/stefan/7786230/working/building/REAL300024450553 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/425 `/scratch/stefan/7786230/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(=O)NCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450553/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450553 none CC1C(NC(=O)C(=O)NCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 49, 42, 42, 24, 43, 24, 24, 8, 1, 1, 1, 1, 49, 49, 49, 49, 49, 53, 53, 99, 133, 201, 201, 201, 201, 201, 49, 49, 49, 49, 49, 43, 24, 8, 8, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 99, 99, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 550 number of broken/clashed sets: 22 ./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: REAL300024450553 none CC1C(NC(=O)C(=O)NCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 86, 86, 86, 121, 121, 121, 198, 201, 201, 80, 80, 80, 77, 40, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 86, 121, 198, 198, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 80, 40, 40, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 809 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450553 none CC1C(NC(=O)C(=O)NCC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 25, 49, 49, 1, 1, 1, 1, 1, 3, 3, 11, 21, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 10, 25, 25, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 11, 11, 80] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 298 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450553 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450553 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450553/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450553 Building REAL300024450554 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450554' /scratch/stefan/7786230/working/building/REAL300024450554 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450554 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450554/0 /scratch/stefan/7786230/working/building/REAL300024450554 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/426 `/scratch/stefan/7786230/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450554/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450554 none CC1C(NC(=O)C2(C)CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 45, 100, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 45, 45, 201] 201 rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 427 number of broken/clashed sets: 23 ./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: REAL300024450554 none CC1C(NC(=O)C2(C)CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [130, 130, 130, 130, 133, 133, 133, 201, 201, 201, 201, 201, 201, 130, 130, 130, 127, 55, 127, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 130, 55, 55, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 636 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450554 none CC1C(NC(=O)C2(C)CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 15, 41, 130, 130, 130, 130, 130, 2, 2, 2, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 15, 15, 130] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450554 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450554 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450554/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450554 Building REAL300024450555 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450555' /scratch/stefan/7786230/working/building/REAL300024450555 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450555 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450555/0 /scratch/stefan/7786230/working/building/REAL300024450555 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/427 `/scratch/stefan/7786230/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450555/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450555 none CC1C(NC(=O)C2CCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 18, 57, 114, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 9, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 57, 57, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 451 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: REAL300024450555 none CC1C(NC(=O)C2CCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 110, 110, 110, 113, 113, 113, 201, 201, 201, 201, 201, 110, 110, 110, 108, 48, 108, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 113, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 110, 48, 48, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 633 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450555 none CC1C(NC(=O)C2CCC(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 33, 110, 110, 110, 110, 110, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 110] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450555 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450555 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450555/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450555 Building REAL300024450556 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450556' /scratch/stefan/7786230/working/building/REAL300024450556 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450556 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450556/0 /scratch/stefan/7786230/working/building/REAL300024450556 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/428 `/scratch/stefan/7786230/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C[NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450556/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450556 none CC1C(NC(=O)C2(C[NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 4, 4, 4, 4, 1, 1, 8, 8, 8, 8, 8, 9, 9, 17, 22, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 17, 17, 30] 30 rigid atoms, others: [4, 6, 7, 44, 42, 43, 12, 13, 45] set([0, 1, 2, 3, 5, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 20 ./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: REAL300024450556 none CC1C(NC(=O)C2(C[NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 24, 24, 24, 30, 30, 30, 30, 30, 30, 30, 23, 23, 23, 21, 15, 21, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 23, 23, 23, 23, 15, 15, 1] 30 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 92 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450556 none CC1C(NC(=O)C2(C[NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 3, 3, 6, 11, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 23] 30 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450556 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450556 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450556/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450556 Building REAL300024450557 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450557' /scratch/stefan/7786230/working/building/REAL300024450557 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450557 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450557/0 /scratch/stefan/7786230/working/building/REAL300024450557 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/429 `/scratch/stefan/7786230/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CNC(=O)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450557/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450557 none CC1C(NC(=O)C2=CNC(=O)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 28, 46, 85, 85, 85, 85, 85, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 85] 85 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 18 ./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: REAL300024450557 none CC1C(NC(=O)C2=CNC(=O)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 85, 85, 85, 85, 85, 85, 85, 85, 85, 81, 81, 81, 76, 40, 76, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 85, 85, 85, 85, 81, 81, 81, 81, 81, 81, 40, 40, 1] 85 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450557 none CC1C(NC(=O)C2=CNC(=O)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 15, 33, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 15, 81] 85 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450557 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450557 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450557/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450557 Building REAL300024450558 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450558' /scratch/stefan/7786230/working/building/REAL300024450558 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450558 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450558/0 /scratch/stefan/7786230/working/building/REAL300024450558 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/430 `/scratch/stefan/7786230/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450558/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450558 none CCCC(CCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [180, 180, 149, 81, 149, 178, 178, 81, 81, 64, 64, 64, 64, 64, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 180, 180, 180, 180, 180, 180, 180, 149, 178, 178, 178, 178, 178, 178, 178, 81, 64, 64, 64, 64, 64, 64, 64, 31, 31, 1, 64, 64, 64, 64] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 926 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450558 none CCCC(CCC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 23, 14, 4, 14, 23, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 64, 64, 64, 64, 64, 1, 1, 24, 24, 24, 24, 24, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 64, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 261 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450558 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450558 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450558/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450558 Building REAL300024450559 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450559' /scratch/stefan/7786230/working/building/REAL300024450559 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450559 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450559/0 /scratch/stefan/7786230/working/building/REAL300024450559 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/431 `/scratch/stefan/7786230/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450559/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450559 none CC1CCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 98, 98, 98, 98, 98, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 98, 1, 2, 2, 2] 137 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 197 number of broken/clashed sets: 32 ./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: REAL300024450559 none CC1CCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 109, 109, 109, 98, 98, 98, 98, 98, 89, 42, 89, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 109, 98, 98, 98, 98, 98, 98, 98, 42, 42, 1, 98, 98, 98, 98] 137 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 457 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450559 none CC1CCCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 13, 13, 47, 76, 137, 137, 137, 137, 137, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 47, 47, 137, 9, 9, 9, 9] 137 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 39, 36, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 331 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450559 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450559 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450559/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450559 Building REAL300024450560 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450560' /scratch/stefan/7786230/working/building/REAL300024450560 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450560 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450560/0 /scratch/stefan/7786230/working/building/REAL300024450560 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/432 `/scratch/stefan/7786230/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450560/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450560 none CC1CCCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 22, 71, 71, 71, 71, 71, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 71, 1, 2, 2, 2, 17, 17] 201 rigid atoms, others: [45, 43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52, 53, 54]) total number of confs: 170 number of broken/clashed sets: 41 ./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: REAL300024450560 none CC1CCCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 72, 72, 72, 71, 71, 71, 71, 71, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 71, 71, 71, 71, 71, 71, 71, 38, 38, 1, 71, 71, 71, 71, 201, 201] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 593 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450560 none CC1CCCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 17, 17, 17, 17, 17, 23, 23, 77, 116, 201, 201, 201, 201, 201, 17, 17, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 17, 17, 17, 17, 77, 77, 201, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 36, 26, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 515 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450560 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450560 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450560/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450560 Building REAL300024450561 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450561' /scratch/stefan/7786230/working/building/REAL300024450561 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450561 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450561/0 /scratch/stefan/7786230/working/building/REAL300024450561 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/433 `/scratch/stefan/7786230/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450561/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450561 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 27, 75, 75, 75, 75, 75, 1, 1, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 75, 1, 2, 2, 2] 156 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 29 ./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: REAL300024450561 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [156, 156, 156, 156, 156, 156, 76, 76, 76, 75, 75, 75, 75, 75, 68, 39, 68, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 156, 156, 156, 156, 156, 156, 76, 75, 75, 75, 75, 75, 75, 75, 39, 39, 1, 75, 75, 75, 75] 156 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 364 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450561 none CC1=NC=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 13, 19, 19, 64, 96, 156, 156, 156, 156, 156, 13, 13, 2, 2, 2, 1, 1, 1, 10, 13, 13, 13, 13, 13, 13, 13, 64, 64, 156, 13, 13, 13, 13] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 410 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450561 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450561 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450561/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450561 Building REAL300024450562 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450562' /scratch/stefan/7786230/working/building/REAL300024450562 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450562 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450562/0 /scratch/stefan/7786230/working/building/REAL300024450562 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/434 `/scratch/stefan/7786230/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450562/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450562 none C=CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 164, 53, 53, 53, 49, 49, 49, 49, 49, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 201, 201, 201, 198, 201, 191, 191, 164, 164, 53, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1, 49, 49, 49, 49] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 871 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450562 none C=CCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 25, 15, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 49, 49, 49, 49, 49, 1, 1, 37, 37, 37, 24, 25, 18, 18, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 254 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450562 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450562 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450562/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450562 Building REAL300024450563 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450563' /scratch/stefan/7786230/working/building/REAL300024450563 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450563 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450563/0 /scratch/stefan/7786230/working/building/REAL300024450563 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/435 `/scratch/stefan/7786230/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450563/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450563 none CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 201, 201, 103, 103, 62, 62, 62, 62, 62, 61, 43, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 62, 62, 62, 62, 62, 62, 62, 43, 43, 1, 62, 62, 62, 62] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 872 number of broken/clashed sets: 58 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450563 none CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 19, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 62, 62, 62, 62, 62, 1, 1, 28, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 1, 2, 2, 2] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 261 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450563 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450563 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450563/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450563 Building REAL300024450564 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450564' /scratch/stefan/7786230/working/building/REAL300024450564 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450564 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450564/0 /scratch/stefan/7786230/working/building/REAL300024450564 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/436 `/scratch/stefan/7786230/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450564/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450564 none CCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 193, 157, 95, 157, 157, 95, 95, 84, 84, 84, 84, 84, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 157, 95, 84, 84, 84, 84, 84, 84, 84, 29, 29, 1, 84, 84, 84, 84] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 885 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450564 none CCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 22, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 84, 84, 84, 84, 84, 1, 1, 25, 25, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 84, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 265 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450564 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450564 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450564/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450564 Building REAL300024450565 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450565' /scratch/stefan/7786230/working/building/REAL300024450565 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450565 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450565/0 /scratch/stefan/7786230/working/building/REAL300024450565 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/437 `/scratch/stefan/7786230/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450565/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450565 none CC1C(NC(=O)C2(C(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 7, 7, 1, 7, 1, 1, 7, 7, 1, 1, 22, 22, 22, 22, 22, 34, 34, 80, 126, 197, 197, 197, 197, 197, 22, 22, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 80, 80, 197] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 10, 11, 36] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 541 number of broken/clashed sets: 88 ./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: REAL300024450565 none CC1C(NC(=O)C2(C(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 107, 107, 107, 197, 201, 201, 197, 197, 64, 64, 64, 62, 44, 62, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 107, 201, 201, 197, 197, 197, 197, 64, 64, 64, 64, 64, 64, 44, 44, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 88 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450565 none CC1C(NC(=O)C2(C(N)=O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 22, 39, 39, 22, 22, 1, 1, 1, 1, 1, 3, 3, 9, 18, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 6, 39, 39, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 9, 9, 64] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 226 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450565 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450565 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450565/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450565 Building REAL300024450566 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450566' /scratch/stefan/7786230/working/building/REAL300024450566 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450566 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450566/0 /scratch/stefan/7786230/working/building/REAL300024450566 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/438 `/scratch/stefan/7786230/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450566/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450566 none CC1C(NC(=O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 156, 156, 156, 201, 201, 201, 201, 201, 156, 156, 156, 148, 61, 148, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 201, 201, 201, 156, 156, 156, 156, 156, 156, 61, 61, 1] 201 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 626 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450566 none CC1C(NC(=O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 10, 10, 1, 1, 1, 1, 1, 4, 4, 16, 51, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 6, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 156] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 9, 10, 11, 12, 34, 13, 35, 26, 27, 31] set([4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450566 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450566 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450566/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450566 Building REAL300024450567 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450567' /scratch/stefan/7786230/working/building/REAL300024450567 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450567 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450567/0 /scratch/stefan/7786230/working/building/REAL300024450567 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/439 `/scratch/stefan/7786230/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450567/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450567 none CC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 36, 98, 98, 98, 98, 98, 1, 1, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 98, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 190 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: REAL300024450567 none CC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 143, 143, 143, 98, 98, 98, 98, 98, 94, 50, 94, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 143, 98, 98, 98, 98, 98, 98, 98, 50, 50, 1, 98, 98, 98, 98] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 551 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450567 none CC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 16, 16, 16, 16, 16, 23, 23, 59, 108, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 10, 16, 16, 16, 16, 16, 16, 16, 59, 59, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 464 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450567 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450567 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450567/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450567 Building REAL300024450568 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450568' /scratch/stefan/7786230/working/building/REAL300024450568 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450568 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450568/0 /scratch/stefan/7786230/working/building/REAL300024450568 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/440 `/scratch/stefan/7786230/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1) `REAL300024450568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450568/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450568 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 82, 82, 82, 82, 82, 1, 1, 10, 10, 23, 23, 23, 23, 23, 10, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 82, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 235 number of broken/clashed sets: 39 ./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: REAL300024450568 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 119, 119, 119, 117, 117, 117, 82, 82, 82, 82, 82, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 119, 119, 201, 201, 201, 201, 201, 119, 117, 82, 82, 82, 82, 82, 82, 82, 39, 39, 1, 82, 82, 82, 82] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 884 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450568 none CCN1C=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 41, 64, 119, 119, 119, 119, 119, 10, 10, 1, 1, 7, 7, 7, 7, 7, 1, 3, 10, 10, 10, 10, 10, 10, 10, 41, 41, 119, 10, 10, 10, 10] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 306 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450568 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450568 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450568/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450568 Building REAL300024450569 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450569' /scratch/stefan/7786230/working/building/REAL300024450569 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450569 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450569/0 /scratch/stefan/7786230/working/building/REAL300024450569 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/441 `/scratch/stefan/7786230/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450569/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450569 none CCC1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 25, 91, 91, 91, 91, 91, 1, 1, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 91, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 41 ./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: REAL300024450569 none CCC1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 138, 138, 138, 91, 91, 91, 91, 91, 84, 42, 84, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 91, 91, 91, 91, 91, 91, 91, 42, 42, 1, 91, 91, 91, 91] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 697 number of broken/clashed sets: 41 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450569 none CCC1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 33, 33, 85, 123, 201, 201, 201, 201, 201, 20, 20, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 20, 85, 85, 201, 20, 20, 20, 20] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 2, 35, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 558 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450569 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450569 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450569/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450569 Building REAL300024450570 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450570' /scratch/stefan/7786230/working/building/REAL300024450570 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450570 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450570/0 /scratch/stefan/7786230/working/building/REAL300024450570 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/442 `/scratch/stefan/7786230/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450570/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450570 none CC(C)C1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 31, 110, 110, 110, 110, 110, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 110, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 223 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: REAL300024450570 none CC(C)C1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 164, 164, 164, 110, 110, 110, 110, 110, 102, 28, 102, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 110, 110, 110, 110, 110, 110, 110, 28, 28, 1, 110, 110, 110, 110] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 629 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450570 none CC(C)C1(C)CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 15, 15, 15, 15, 15, 24, 24, 72, 116, 201, 201, 201, 201, 201, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 72, 72, 201, 15, 15, 15, 15] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 500 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450570 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450570 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450570/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450570 Building REAL300024450571 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450571' /scratch/stefan/7786230/working/building/REAL300024450571 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450571 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450571/0 /scratch/stefan/7786230/working/building/REAL300024450571 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/443 `/scratch/stefan/7786230/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450571/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450571 none COCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 180, 179, 180, 81, 81, 81, 69, 69, 69, 69, 69, 67, 27, 67, 12, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 201, 180, 180, 180, 180, 179, 179, 81, 69, 69, 69, 69, 69, 69, 69, 27, 27, 1, 69, 69, 69, 69] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 795 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450571 none COCC(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 31, 24, 15, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 69, 69, 69, 69, 69, 1, 1, 35, 35, 35, 31, 31, 24, 24, 24, 24, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 264 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450571 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450571 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450571/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450571 Building REAL300024450572 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450572' /scratch/stefan/7786230/working/building/REAL300024450572 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450572 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450572/0 /scratch/stefan/7786230/working/building/REAL300024450572 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/444 `/scratch/stefan/7786230/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450572/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450572 none COCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 195, 125, 195, 195, 125, 125, 88, 88, 88, 88, 88, 84, 30, 84, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 125, 88, 88, 88, 88, 88, 88, 88, 30, 30, 1, 88, 88, 88, 88] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 827 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450572 none COCCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 15, 15, 11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 88, 88, 88, 88, 88, 1, 1, 26, 26, 26, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 88, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450572 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450572 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450572/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450572 Building REAL300024450573 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450573' /scratch/stefan/7786230/working/building/REAL300024450573 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450573 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450573/0 /scratch/stefan/7786230/working/building/REAL300024450573 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/445 `/scratch/stefan/7786230/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1) `REAL300024450573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450573/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450573 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 19 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: REAL300024450573 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450573 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450573 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450573 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450573/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450573 Building REAL300024450574 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450574' /scratch/stefan/7786230/working/building/REAL300024450574 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450574 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450574/0 /scratch/stefan/7786230/working/building/REAL300024450574 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/446 `/scratch/stefan/7786230/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NON=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450574/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450574 none CC1=NON=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 26, 26, 26, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 84, 84, 84, 84, 84, 1, 1, 26, 26, 26, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 84, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 212 number of broken/clashed sets: 6 ./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: REAL300024450574 none CC1=NON=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 117, 117, 117, 84, 84, 84, 84, 84, 79, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 117, 84, 84, 84, 84, 84, 84, 84, 30, 30, 1, 84, 84, 84, 84] 201 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 807 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450574 none CC1=NON=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 19, 19, 19, 26, 26, 26, 26, 26, 39, 39, 81, 123, 201, 201, 201, 201, 201, 26, 26, 2, 2, 2, 6, 6, 19, 26, 26, 26, 26, 26, 26, 26, 81, 81, 201, 26, 26, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450574 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450574 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450574/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450574 Building REAL300024450575 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450575' /scratch/stefan/7786230/working/building/REAL300024450575 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450575 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450575/0 /scratch/stefan/7786230/working/building/REAL300024450575 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/447 `/scratch/stefan/7786230/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450575/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450575 none CC1C(NC(=O)CCC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 28, 28, 6, 28, 4, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 42, 42, 96, 133, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 28, 6, 6, 4, 4, 2, 2, 2, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 96, 96, 201] 201 rigid atoms, others: [39, 8, 9, 10, 11, 40, 41, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 578 number of broken/clashed sets: 39 ./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: REAL300024450575 none CC1C(NC(=O)CCC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 68, 68, 68, 145, 146, 201, 201, 201, 50, 50, 50, 48, 30, 48, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 68, 145, 145, 146, 146, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 50, 30, 30, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 809 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450575 none CC1C(NC(=O)CCC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 19, 35, 35, 35, 1, 1, 1, 1, 1, 3, 3, 8, 13, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 4, 16, 16, 19, 19, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 8, 8, 50] 201 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450575 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450575 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450575/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450575 Building REAL300024450576 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450576' /scratch/stefan/7786230/working/building/REAL300024450576 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450576 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450576/0 /scratch/stefan/7786230/working/building/REAL300024450576 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/448 `/scratch/stefan/7786230/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1) `REAL300024450576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450576/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450576 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 39, 121, 121, 121, 121, 121, 1, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 121, 1, 2, 2, 2, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 24 ./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: REAL300024450576 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 196, 196, 121, 121, 121, 121, 121, 119, 52, 119, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 196, 121, 121, 121, 121, 121, 121, 121, 52, 52, 1, 121, 121, 121, 121, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 631 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450576 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 12, 12, 12, 12, 12, 20, 20, 59, 110, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 12, 12, 59, 59, 201, 12, 12, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 460 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450576 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450576 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450576/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450576 Building REAL300024450577 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450577' /scratch/stefan/7786230/working/building/REAL300024450577 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450577 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450577/0 /scratch/stefan/7786230/working/building/REAL300024450577 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/449 `/scratch/stefan/7786230/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450577/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450577 none CC1C(NC(=O)C2(C)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 35, 94, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 35, 35, 201] 201 rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 45, 44, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 400 number of broken/clashed sets: 27 ./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: REAL300024450577 none CC1C(NC(=O)C2(C)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 126, 126, 126, 201, 201, 201, 201, 201, 201, 124, 124, 124, 120, 54, 120, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 124, 54, 54, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 683 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450577 none CC1C(NC(=O)C2(C)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 13, 38, 124, 124, 124, 124, 124, 2, 2, 2, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 124] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450577 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450577 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450577/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450577 Building REAL300024450578 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450578' /scratch/stefan/7786230/working/building/REAL300024450578 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450578 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450578/0 /scratch/stefan/7786230/working/building/REAL300024450578 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/450 `/scratch/stefan/7786230/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450578/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450578 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 37, 37, 82, 103, 141, 141, 141, 141, 141, 27, 27, 27, 27, 27, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 82, 82, 141] 141 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 44, 43, 45, 36, 38, 42] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 433 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: REAL300024450578 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 52, 52, 52, 81, 81, 81, 141, 141, 141, 141, 141, 141, 141, 52, 52, 52, 52, 32, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 81, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 52, 52, 52, 52, 52, 52, 32, 32, 1] 141 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 469 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450578 none CC1C(NC(=O)C2CC[NH+](C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 9, 17, 52, 52, 52, 52, 52, 2, 2, 2, 1, 1, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 9, 9, 52] 141 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450578 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450578 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450578/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450578 Building REAL300024450579 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450579' /scratch/stefan/7786230/working/building/REAL300024450579 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450579 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450579/0 /scratch/stefan/7786230/working/building/REAL300024450579 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/451 `/scratch/stefan/7786230/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450579/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450579 none CC1C(NC(=O)C2(C)CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 49, 98, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 49, 49, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 439 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: REAL300024450579 none CC1C(NC(=O)C2(C)CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [113, 113, 113, 113, 131, 131, 131, 201, 201, 201, 201, 201, 113, 113, 113, 110, 50, 110, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 113, 113, 50, 50, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 625 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450579 none CC1C(NC(=O)C2(C)CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 11, 34, 113, 113, 113, 113, 113, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 113] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450579 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450579 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450579/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450579 Building REAL300024450580 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450580' /scratch/stefan/7786230/working/building/REAL300024450580 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450580 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450580/0 /scratch/stefan/7786230/working/building/REAL300024450580 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/452 `/scratch/stefan/7786230/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450580/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450580 none CC1C(NC(=O)C2=CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 18, 18, 44, 63, 97, 97, 97, 97, 97, 13, 13, 13, 13, 13, 9, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 13, 44, 44, 97] 97 rigid atoms, others: [33, 4, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 263 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: REAL300024450580 none CC1C(NC(=O)C2=CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 63, 63, 63, 97, 97, 97, 97, 97, 97, 60, 60, 60, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 63, 97, 97, 97, 97, 97, 60, 60, 60, 60, 60, 60, 36, 36, 1] 97 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450580 none CC1C(NC(=O)C2=CN(C)C(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 12, 22, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 60] 97 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450580 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450580 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450580/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450580 Building REAL300024450581 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450581' /scratch/stefan/7786230/working/building/REAL300024450581 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450581 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450581/0 /scratch/stefan/7786230/working/building/REAL300024450581 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/453 `/scratch/stefan/7786230/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450581/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450581 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 6 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450581 none COC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 33 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450581 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450581 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450581/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450581 Building REAL300024450582 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450582' /scratch/stefan/7786230/working/building/REAL300024450582 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450582 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450582/0 /scratch/stefan/7786230/working/building/REAL300024450582 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/454 `/scratch/stefan/7786230/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450582/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450582 none CC1CC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 38, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 79, 79, 79, 79, 79, 1, 1, 38, 38, 38, 38, 38, 38, 38, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 79, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 257 number of broken/clashed sets: 18 ./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: REAL300024450582 none CC1CC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 87, 87, 87, 79, 79, 79, 79, 79, 72, 26, 72, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 201, 201, 193, 193, 87, 79, 79, 79, 79, 79, 79, 79, 26, 26, 1, 79, 79, 79, 79] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 748 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450582 none CC1CC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 30, 30, 30, 38, 38, 38, 38, 38, 53, 53, 101, 148, 201, 201, 201, 201, 201, 38, 38, 2, 2, 2, 1, 1, 1, 1, 5, 5, 30, 38, 38, 38, 38, 38, 38, 38, 101, 101, 201, 38, 38, 38, 38] 201 rigid atoms, others: [0, 1, 2, 3, 4, 28, 29, 30, 31] set([5, 6, 7, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 576 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450582 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450582 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450582/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450582 Building REAL300024450583 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450583' /scratch/stefan/7786230/working/building/REAL300024450583 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450583 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450583/0 /scratch/stefan/7786230/working/building/REAL300024450583 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/455 `/scratch/stefan/7786230/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450583/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450583 none CCCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 22, 19, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 62, 62, 62, 62, 62, 1, 1, 15, 15, 23, 23, 23, 23, 23, 22, 22, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 62, 1, 2, 2, 2, 15, 15, 15, 15] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 6 ./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: REAL300024450583 none CCCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 198, 189, 84, 84, 84, 62, 62, 62, 62, 62, 61, 27, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 189, 189, 201, 201, 201, 201, 201, 201, 201, 198, 198, 84, 62, 62, 62, 62, 62, 62, 62, 27, 27, 1, 62, 62, 62, 62, 189, 189, 189, 189] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 650 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450583 none CCCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 4, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 24, 24, 51, 91, 189, 189, 189, 189, 189, 15, 15, 1, 1, 6, 6, 6, 6, 6, 5, 5, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 51, 51, 189, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 457 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450583 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450583 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450583/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450583 Building REAL300024450584 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450584' /scratch/stefan/7786230/working/building/REAL300024450584 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450584 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450584/0 /scratch/stefan/7786230/working/building/REAL300024450584 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/456 `/scratch/stefan/7786230/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450584/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450584 none C=C1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 24, 71, 71, 71, 71, 71, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 71, 1, 2, 2, 2, 26, 26, 26, 26] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 36 ./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: REAL300024450584 none C=C1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 95, 95, 71, 71, 71, 71, 71, 66, 37, 66, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 71, 71, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71, 71, 71, 201, 201, 201, 201] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 640 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450584 none C=C1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 26, 26, 26, 26, 26, 37, 37, 92, 127, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26, 26, 26, 26, 26, 92, 92, 201, 26, 26, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 49, 50, 51, 52, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 553 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450584 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450584 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450584/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450584 Building REAL300024450585 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450585' /scratch/stefan/7786230/working/building/REAL300024450585 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450585 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450585/0 /scratch/stefan/7786230/working/building/REAL300024450585 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/457 `/scratch/stefan/7786230/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450585/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450585 none C=CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 18, 15, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 1, 1, 9, 9, 29, 29, 29, 18, 18, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 58, 1, 2, 2, 2, 9, 9, 9, 9] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 218 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: REAL300024450585 none C=CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 194, 184, 77, 77, 77, 58, 58, 58, 58, 58, 54, 26, 54, 12, 1, 1, 1, 1, 1, 1, 1, 58, 58, 184, 184, 201, 201, 201, 201, 201, 194, 194, 77, 58, 58, 58, 58, 58, 58, 58, 26, 26, 1, 58, 58, 58, 58, 184, 184, 184, 184] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 664 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450585 none C=CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 17, 17, 41, 74, 184, 184, 184, 184, 184, 9, 9, 1, 1, 11, 11, 11, 6, 6, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 41, 41, 184, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 430 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450585 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450585 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450585/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450585 Building REAL300024450586 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450586' /scratch/stefan/7786230/working/building/REAL300024450586 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450586 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450586/0 /scratch/stefan/7786230/working/building/REAL300024450586 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/458 `/scratch/stefan/7786230/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450586/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450586 none C=CC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 109, 196, 196, 192, 109, 109, 60, 60, 60, 60, 60, 59, 47, 59, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 196, 196, 196, 201, 201, 201, 201, 201, 109, 60, 60, 60, 60, 60, 60, 60, 47, 47, 1, 60, 60, 60, 60] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 883 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450586 none C=CC(C)(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 6, 19, 19, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 60, 60, 60, 60, 60, 1, 1, 29, 29, 29, 19, 19, 19, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 269 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450586 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450586 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450586/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450586 Building REAL300024450587 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450587' /scratch/stefan/7786230/working/building/REAL300024450587 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450587 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450587/0 /scratch/stefan/7786230/working/building/REAL300024450587 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/459 `/scratch/stefan/7786230/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450587/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450587 none CC1C(NC(=O)C2CCC(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 36, 36, 94, 129, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 94, 94, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 556 number of broken/clashed sets: 38 ./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: REAL300024450587 none CC1C(NC(=O)C2CCC(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 93, 93, 93, 201, 201, 201, 201, 201, 201, 71, 71, 71, 67, 40, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 71, 40, 40, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 667 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450587 none CC1C(NC(=O)C2CCC(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 13, 21, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 13, 13, 71] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450587 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450587 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450587/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450587 Building REAL300024450588 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450588' /scratch/stefan/7786230/working/building/REAL300024450588 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450588 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450588/0 /scratch/stefan/7786230/working/building/REAL300024450588 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/460 `/scratch/stefan/7786230/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[C@H]2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450588/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450588 none CC1C(NC(=O)C[C@H]2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 26, 26, 6, 26, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 48, 48, 95, 133, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 26, 6, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 95, 95, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 567 number of broken/clashed sets: 25 ./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: REAL300024450588 none CC1C(NC(=O)C[C@H]2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 80, 80, 80, 166, 201, 201, 201, 201, 201, 71, 71, 71, 61, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 80, 166, 166, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 71, 26, 26, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 768 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450588 none CC1C(NC(=O)C[C@H]2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 10, 18, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 18, 18, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 10, 10, 71] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450588 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450588 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450588/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450588 Building REAL300024450589 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450589' /scratch/stefan/7786230/working/building/REAL300024450589 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450589 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450589/0 /scratch/stefan/7786230/working/building/REAL300024450589 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/461 `/scratch/stefan/7786230/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450589/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450589 none C=CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 15, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 90, 90, 90, 90, 90, 1, 1, 8, 8, 8, 24, 24, 24, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 90, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 242 number of broken/clashed sets: 50 ./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: REAL300024450589 none C=CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 193, 113, 113, 113, 90, 90, 90, 90, 90, 83, 26, 83, 12, 1, 1, 1, 1, 1, 1, 1, 90, 90, 193, 193, 193, 201, 201, 201, 201, 201, 113, 90, 90, 90, 90, 90, 90, 90, 26, 26, 1, 90, 90, 90, 90, 193, 193, 193, 193, 193, 193] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 667 number of broken/clashed sets: 50 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450589 none C=CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 14, 14, 45, 82, 193, 193, 193, 193, 193, 8, 8, 1, 1, 1, 13, 13, 13, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 45, 45, 193, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 445 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450589 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450589 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450589/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450589 Building REAL300024450590 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450590' /scratch/stefan/7786230/working/building/REAL300024450590 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450590 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450590/0 /scratch/stefan/7786230/working/building/REAL300024450590 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/462 `/scratch/stefan/7786230/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450590/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450590 none CC1C(NC(=O)CC2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 24, 24, 6, 24, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 49, 49, 96, 133, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 96, 96, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 565 number of broken/clashed sets: 22 ./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: REAL300024450590 none CC1C(NC(=O)CC2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 72, 83, 83, 83, 201, 201, 201, 201, 201, 201, 72, 72, 72, 64, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 72, 72, 28, 28, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 735 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450590 none CC1C(NC(=O)CC2=CCOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 19, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 3, 16, 16, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 72] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450590 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450590 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450590/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450590 Building REAL300024450591 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450591' /scratch/stefan/7786230/working/building/REAL300024450591 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450591 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450591/0 /scratch/stefan/7786230/working/building/REAL300024450591 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/463 `/scratch/stefan/7786230/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1) `REAL300024450591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450591/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450591 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 27, 115, 115, 115, 115, 115, 1, 1, 13, 13, 13, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 115, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 269 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: REAL300024450591 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 169, 169, 161, 161, 161, 115, 115, 115, 115, 115, 108, 31, 108, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 169, 169, 169, 201, 201, 201, 201, 201, 161, 115, 115, 115, 115, 115, 115, 115, 31, 31, 1, 115, 115, 115, 115, 169, 169] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 700 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450591 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 19, 19, 53, 81, 169, 169, 169, 169, 169, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 53, 53, 169, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 384 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450591 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450591 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450591/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450591 Building REAL300024450592 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450592' /scratch/stefan/7786230/working/building/REAL300024450592 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450592 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450592/0 /scratch/stefan/7786230/working/building/REAL300024450592 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/464 `/scratch/stefan/7786230/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450592/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450592 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 21 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: REAL300024450592 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 4, 4, 4, 4] 4 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 9 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450592 none CCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 4 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 23, 24] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450592 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450592 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450592/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450592 Building REAL300024450593 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450593' /scratch/stefan/7786230/working/building/REAL300024450593 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450593 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450593/0 /scratch/stefan/7786230/working/building/REAL300024450593 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/465 `/scratch/stefan/7786230/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450593/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450593 none CC(C)[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 55, 54, 63, 54, 54, 41, 41, 41, 41, 41, 41, 29, 41, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 63, 63, 62, 63, 63, 63, 63, 63, 63, 63, 63, 54, 41, 41, 41, 41, 41, 41, 41, 29, 29, 1, 41, 41, 41, 41, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 301 number of broken/clashed sets: 62 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450593 none CC(C)[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 9, 7, 6, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 41, 41, 41, 41, 41, 1, 1, 9, 10, 9, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 41, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10] 63 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 150 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450593 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450593 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450593/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450593 Building REAL300024450594 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450594' /scratch/stefan/7786230/working/building/REAL300024450594 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450594 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450594/0 /scratch/stefan/7786230/working/building/REAL300024450594 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/466 `/scratch/stefan/7786230/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450594/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450594 none CCC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 88, 88, 88, 88, 88, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 15, 15, 88, 1, 2, 2, 2] 95 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 170 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: REAL300024450594 none CCC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 95, 95, 95, 95, 95, 88, 88, 88, 88, 88, 88, 88, 88, 82, 38, 82, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 88, 88, 88, 88, 88, 88, 88, 88, 38, 38, 1, 88, 88, 88, 88] 95 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 305 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450594 none CCC1CCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 6, 6, 28, 49, 95, 95, 95, 95, 95, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 28, 28, 95, 4, 4, 4, 4] 95 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 38, 39, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 222 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450594 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450594 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450594/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450594 Building REAL300024450595 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450595' /scratch/stefan/7786230/working/building/REAL300024450595 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450595 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450595/0 /scratch/stefan/7786230/working/building/REAL300024450595 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/467 `/scratch/stefan/7786230/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450595/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450595 none CC1CCCC1(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 8, 6, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 47, 157, 157, 157, 157, 157, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 157, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 258 number of broken/clashed sets: 32 ./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: REAL300024450595 none CC1CCCC1(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 191, 201, 191, 191, 157, 157, 157, 157, 157, 151, 66, 151, 13, 1, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 157, 157, 157, 157, 157, 157, 157, 66, 66, 1, 157, 157, 157, 157] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 627 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450595 none CC1CCCC1(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 8, 8, 8, 8, 8, 14, 14, 46, 104, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 46, 46, 201, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 439 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450595 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450595 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450595/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450595 Building REAL300024450596 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450596' /scratch/stefan/7786230/working/building/REAL300024450596 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450596 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450596/0 /scratch/stefan/7786230/working/building/REAL300024450596 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/468 `/scratch/stefan/7786230/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450596/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450596 none CC1C(NC(=O)CC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 72, 72, 72, 140, 188, 201, 201, 50, 50, 50, 50, 37, 50, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 72, 140, 140, 201, 201, 201, 50, 50, 50, 50, 50, 50, 37, 37, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 1011 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450596 none CC1C(NC(=O)CC(C)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 19, 29, 32, 32, 1, 1, 1, 1, 1, 3, 3, 9, 15, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 4, 19, 19, 32, 32, 32, 1, 1, 1, 1, 1, 1, 9, 9, 50] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450596 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450596 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450596/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450596 Building REAL300024450597 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450597' /scratch/stefan/7786230/working/building/REAL300024450597 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450597 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450597/0 /scratch/stefan/7786230/working/building/REAL300024450597 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/469 `/scratch/stefan/7786230/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450597/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450597 none COC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 140, 201, 201, 201, 201, 140, 140, 115, 115, 115, 115, 115, 108, 44, 108, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 115, 115, 115, 115, 115, 115, 115, 44, 44, 1, 115, 115, 115, 115] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 760 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450597 none COC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 18, 4, 18, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 23, 115, 115, 115, 115, 115, 1, 1, 19, 19, 19, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 115, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 264 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450597 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450597 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450597/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450597 Building REAL300024450598 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450598' /scratch/stefan/7786230/working/building/REAL300024450598 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450598 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450598/0 /scratch/stefan/7786230/working/building/REAL300024450598 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/470 `/scratch/stefan/7786230/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450598/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450598 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 21, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 77, 77, 77, 77, 77, 1, 1, 15, 15, 25, 25, 25, 25, 25, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 77, 1, 2, 2, 2, 15, 15, 15, 15] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 10 ./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: REAL300024450598 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 192, 91, 91, 91, 77, 77, 77, 77, 77, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 192, 192, 201, 201, 201, 201, 201, 201, 201, 91, 77, 77, 77, 77, 77, 77, 77, 30, 30, 1, 77, 77, 77, 77, 192, 192, 192, 192] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 663 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450598 none CCCC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 4, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 22, 22, 58, 93, 192, 192, 192, 192, 192, 15, 15, 1, 1, 5, 5, 5, 5, 5, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 58, 58, 192, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 48, 49, 50, 51, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 448 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450598 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450598 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450598/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450598 Building REAL300024450599 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450599' /scratch/stefan/7786230/working/building/REAL300024450599 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450599 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450599/0 /scratch/stefan/7786230/working/building/REAL300024450599 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/471 `/scratch/stefan/7786230/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@]2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450599/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450599 none CC1C(NC(=O)[C@]2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 20, 20, 52, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 7, 2, 2, 2, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 52, 52, 201] 201 rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 40, 36, 38] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 452 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: REAL300024450599 none CC1C(NC(=O)[C@]2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [143, 143, 143, 143, 186, 186, 186, 201, 201, 201, 201, 201, 201, 143, 143, 143, 139, 59, 139, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 186, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 143, 59, 59, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 646 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450599 none CC1C(NC(=O)[C@]2(C)CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 12, 41, 143, 143, 143, 143, 143, 2, 2, 2, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 12, 143] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 256 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450599 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450599 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450599/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450599 Building REAL300024450600 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450600' /scratch/stefan/7786230/working/building/REAL300024450600 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450600 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450600/0 /scratch/stefan/7786230/working/building/REAL300024450600 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/472 `/scratch/stefan/7786230/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450600/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450600 none CCC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 13, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 91, 91, 91, 91, 91, 1, 1, 29, 29, 29, 29, 29, 13, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 91, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 243 number of broken/clashed sets: 29 ./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: REAL300024450600 none CCC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 147, 147, 147, 147, 147, 100, 100, 100, 91, 91, 91, 91, 91, 79, 29, 79, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 147, 100, 91, 91, 91, 91, 91, 91, 91, 29, 29, 1, 91, 91, 91, 91] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 700 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450600 none CCC1=NOC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 13, 19, 19, 54, 80, 147, 147, 147, 147, 147, 13, 13, 6, 6, 6, 5, 5, 1, 9, 13, 13, 13, 13, 13, 13, 13, 54, 54, 147, 13, 13, 13, 13] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 379 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450600 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450600 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450600/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450600 Building REAL300024450601 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450601' /scratch/stefan/7786230/working/building/REAL300024450601 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450601 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450601/0 /scratch/stefan/7786230/working/building/REAL300024450601 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/473 `/scratch/stefan/7786230/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450601/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450601 none CC1COCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 39, 150, 150, 150, 150, 150, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 150, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 258 number of broken/clashed sets: 14 ./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: REAL300024450601 none CC1COCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 169, 169, 169, 150, 150, 150, 150, 150, 147, 67, 147, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 150, 150, 150, 150, 150, 150, 150, 67, 67, 1, 150, 150, 150, 150] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 662 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450601 none CC1COCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 12, 12, 12, 12, 12, 18, 18, 49, 105, 201, 201, 201, 201, 201, 12, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 49, 49, 201, 12, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 433 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450601 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450601 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450601/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450601 Building REAL300024450602 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450602' /scratch/stefan/7786230/working/building/REAL300024450602 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450602 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450602/0 /scratch/stefan/7786230/working/building/REAL300024450602 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/474 `/scratch/stefan/7786230/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450602/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450602 none CC1C(NC(=O)C2=CC=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 50, 104, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 50, 50, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 425 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: REAL300024450602 none CC1C(NC(=O)C2=CC=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [148, 148, 148, 148, 162, 162, 162, 201, 201, 201, 201, 201, 148, 148, 148, 143, 62, 143, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 162, 201, 201, 201, 148, 148, 148, 148, 148, 148, 62, 62, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 571 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450602 none CC1C(NC(=O)C2=CC=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 14, 45, 148, 148, 148, 148, 148, 2, 2, 2, 1, 1, 4, 11, 11, 11, 1, 1, 1, 1, 1, 1, 14, 14, 148] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450602 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450602 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450602/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450602 Building REAL300024450603 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450603' /scratch/stefan/7786230/working/building/REAL300024450603 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450603 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450603/0 /scratch/stefan/7786230/working/building/REAL300024450603 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/475 `/scratch/stefan/7786230/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450603/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450603 none COCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 81, 180, 186, 81, 81, 64, 64, 64, 64, 64, 64, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 180, 186, 186, 186, 81, 64, 64, 64, 64, 64, 64, 64, 37, 37, 1, 64, 64, 64, 64] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 830 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450603 none COCC(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 15, 10, 3, 10, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 64, 64, 64, 64, 64, 1, 1, 24, 24, 24, 15, 15, 10, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 64, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450603 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450603 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450603/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450603 Building REAL300024450604 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450604' /scratch/stefan/7786230/working/building/REAL300024450604 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450604 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450604/0 /scratch/stefan/7786230/working/building/REAL300024450604 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/476 `/scratch/stefan/7786230/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450604/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450604 none CC1C(NC(=O)C2CCC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 34, 34, 84, 115, 189, 189, 189, 189, 189, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 84, 84, 189] 189 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 531 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: REAL300024450604 none CC1C(NC(=O)C2CCC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 98, 98, 98, 189, 189, 189, 189, 189, 189, 67, 67, 67, 64, 38, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 98, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 67, 67, 67, 67, 67, 67, 38, 38, 1] 189 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 597 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450604 none CC1C(NC(=O)C2CCC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 12, 20, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 12, 12, 67] 189 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450604 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450604 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450604/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450604 Building REAL300024450605 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450605' /scratch/stefan/7786230/working/building/REAL300024450605 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450605 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450605/0 /scratch/stefan/7786230/working/building/REAL300024450605 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/477 `/scratch/stefan/7786230/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCO1) `REAL300024450605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450605/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450605 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [190, 122, 122, 122, 108, 108, 108, 108, 108, 94, 28, 94, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 190, 201, 201, 201, 201, 190, 190, 190, 190, 122, 108, 108, 108, 108, 108, 108, 108, 28, 28, 1, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 758 number of broken/clashed sets: 20 ./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: REAL300024450605 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 16, 16, 16, 22, 22, 22, 22, 22, 32, 32, 87, 130, 201, 201, 201, 201, 201, 22, 22, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 22, 22, 22, 22, 22, 22, 22, 87, 87, 201, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 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]) total number of confs: 537 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450605 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 108, 108, 108, 108, 108, 1, 1, 15, 22, 22, 22, 22, 15, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 108, 1, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 248 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450605 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450605 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450605/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450605 Building REAL300024450606 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450606' /scratch/stefan/7786230/working/building/REAL300024450606 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450606 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450606/0 /scratch/stefan/7786230/working/building/REAL300024450606 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/478 `/scratch/stefan/7786230/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450606/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450606 none CCC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 12, 12, 12, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 67, 67, 67, 67, 67, 1, 1, 40, 40, 40, 40, 40, 36, 36, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2] 201 rigid atoms, others: [48, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 272 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: REAL300024450606 none CCC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 147, 147, 147, 147, 68, 147, 68, 68, 67, 67, 67, 67, 67, 60, 25, 60, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 147, 147, 68, 67, 67, 67, 67, 67, 67, 67, 25, 25, 1, 67, 67, 67, 67] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 758 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450606 none CCC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 21, 21, 47, 83, 147, 147, 147, 147, 147, 12, 12, 10, 10, 10, 10, 10, 6, 6, 1, 1, 11, 12, 12, 12, 12, 12, 12, 12, 47, 47, 147, 12, 12, 12, 12] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 3, 36] set([0, 1, 9, 10, 11, 12, 13, 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 397 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450606 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450606 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450606/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450606 Building REAL300024450607 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450607' /scratch/stefan/7786230/working/building/REAL300024450607 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450607 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450607/0 /scratch/stefan/7786230/working/building/REAL300024450607 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/479 `/scratch/stefan/7786230/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC2CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450607/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450607 none CC1C(NC(=O)C23CC2CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 45, 98, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 45, 45, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 416 number of broken/clashed sets: 28 ./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: REAL300024450607 none CC1C(NC(=O)C23CC2CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 122, 122, 122, 201, 201, 201, 201, 201, 201, 117, 117, 117, 114, 55, 114, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 55, 55, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 510 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450607 none CC1C(NC(=O)C23CC2CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 12, 36, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 117] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450607 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450607 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450607/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450607 Building REAL300024450608 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450608' /scratch/stefan/7786230/working/building/REAL300024450608 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450608 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450608/0 /scratch/stefan/7786230/working/building/REAL300024450608 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/480 `/scratch/stefan/7786230/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450608/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450608 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 15 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: REAL300024450608 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 3 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450608 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 2 rigid atoms, others: [1, 3, 4, 48, 49, 50, 51, 24, 25] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 11 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450608 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450608 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450608/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450608 Building REAL300024450609 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450609' /scratch/stefan/7786230/working/building/REAL300024450609 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450609 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450609/0 /scratch/stefan/7786230/working/building/REAL300024450609 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/481 `/scratch/stefan/7786230/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450609/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450609 none C=C1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 67, 67, 67, 67, 67, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 23 ./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: REAL300024450609 none C=C1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 201, 70, 70, 67, 67, 67, 67, 67, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 70, 67, 67, 67, 67, 67, 67, 67, 36, 36, 1, 67, 67, 67, 67, 201, 201] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 593 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450609 none C=C1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 13, 13, 13, 13, 13, 19, 19, 50, 94, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 6, 13, 13, 13, 13, 13, 13, 13, 50, 50, 201, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 25, 26, 27, 28, 29] set([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]) total number of confs: 445 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450609 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450609 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450609/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450609 Building REAL300024450610 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450610' /scratch/stefan/7786230/working/building/REAL300024450610 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450610 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450610/0 /scratch/stefan/7786230/working/building/REAL300024450610 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/482 `/scratch/stefan/7786230/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450610/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450610 none CC1C(NC(=O)C(C)(C)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 100, 100, 100, 201, 201, 201, 201, 201, 58, 58, 58, 57, 42, 57, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 100, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 42, 42, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 815 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450610 none CC1C(NC(=O)C(C)(C)C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 16, 16, 16, 27, 27, 1, 1, 1, 1, 1, 3, 3, 11, 18, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 6, 16, 16, 16, 16, 16, 16, 27, 1, 1, 1, 1, 1, 1, 11, 11, 58] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450610 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450610 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450610/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450610 Building REAL300024450611 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450611' /scratch/stefan/7786230/working/building/REAL300024450611 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450611 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450611/0 /scratch/stefan/7786230/working/building/REAL300024450611 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/483 `/scratch/stefan/7786230/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1) `REAL300024450611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450611/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450611 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 79, 79, 79, 79, 79, 1, 1, 38, 38, 38, 38, 38, 38, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 79, 1, 2, 2, 2, 38, 38] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 217 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: REAL300024450611 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 189, 105, 105, 105, 79, 79, 79, 79, 79, 75, 29, 75, 12, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 201, 189, 189, 105, 79, 79, 79, 79, 79, 79, 79, 29, 29, 1, 79, 79, 79, 79, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48]) total number of confs: 773 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450611 none CC1=C(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=C1 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 27, 27, 27, 38, 38, 38, 38, 38, 51, 51, 89, 126, 201, 201, 201, 201, 201, 38, 38, 1, 1, 1, 2, 2, 2, 5, 5, 27, 38, 38, 38, 38, 38, 38, 38, 89, 89, 201, 38, 38, 38, 38, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 538 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450611 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450611 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450611/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450611 Building REAL300024450612 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450612' /scratch/stefan/7786230/working/building/REAL300024450612 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450612 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450612/0 /scratch/stefan/7786230/working/building/REAL300024450612 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/484 `/scratch/stefan/7786230/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1) `REAL300024450612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450612/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450612 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 29, 124, 124, 124, 124, 124, 1, 1, 12, 12, 12, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 124, 1, 2, 2, 2, 12] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 278 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: REAL300024450612 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 196, 177, 177, 177, 124, 124, 124, 124, 124, 113, 31, 113, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 196, 196, 196, 201, 201, 201, 201, 201, 177, 124, 124, 124, 124, 124, 124, 124, 31, 31, 1, 124, 124, 124, 124, 196] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47]) total number of confs: 594 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450612 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 20, 20, 55, 90, 196, 196, 196, 196, 196, 12, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 55, 55, 196, 12, 12, 12, 12, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 443 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450612 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450612 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450612/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450612 Building REAL300024450613 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450613' /scratch/stefan/7786230/working/building/REAL300024450613 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450613 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450613/0 /scratch/stefan/7786230/working/building/REAL300024450613 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/485 `/scratch/stefan/7786230/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450613/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450613 none CC1C(NC(=O)C2(CF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 7, 7, 1, 7, 1, 1, 9, 1, 1, 26, 26, 26, 26, 26, 38, 38, 84, 120, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 7, 9, 9, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 84, 84, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 9, 10, 36] set([0, 1, 2, 3, 5, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 558 number of broken/clashed sets: 88 ./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: REAL300024450613 none CC1C(NC(=O)C2(CF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 108, 108, 108, 201, 201, 201, 201, 58, 58, 58, 56, 43, 56, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 108, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 43, 43, 1] 201 rigid atoms, others: [45, 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, 43, 44]) total number of confs: 660 number of broken/clashed sets: 88 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450613 none CC1C(NC(=O)C2(CF)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 26, 47, 26, 26, 1, 1, 1, 1, 1, 3, 3, 9, 17, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 6, 47, 47, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 9, 9, 58] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450613 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450613 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450613/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450613 Building REAL300024450614 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450614' /scratch/stefan/7786230/working/building/REAL300024450614 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450614 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450614/0 /scratch/stefan/7786230/working/building/REAL300024450614 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/486 `/scratch/stefan/7786230/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450614/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450614 none CC1C(NC(=O)C2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 34, 34, 88, 125, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 88, 88, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 552 number of broken/clashed sets: 34 ./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: REAL300024450614 none CC1C(NC(=O)C2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 86, 86, 86, 201, 201, 201, 201, 201, 68, 68, 68, 65, 39, 65, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 68, 39, 39, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 648 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450614 none CC1C(NC(=O)C2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 13, 21, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 13, 13, 68] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450614 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450614 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450614/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450614 Building REAL300024450615 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450615' /scratch/stefan/7786230/working/building/REAL300024450615 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450615 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450615/0 /scratch/stefan/7786230/working/building/REAL300024450615 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/487 `/scratch/stefan/7786230/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450615/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450615 none CC1C(NC(=O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [166, 166, 166, 166, 167, 167, 167, 201, 201, 201, 166, 166, 166, 155, 66, 155, 13, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 166, 166, 166, 166, 66, 66, 1] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 707 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450615 none CC1C(NC(=O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 17, 60, 166, 166, 166, 166, 166, 2, 2, 2, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 17, 17, 166] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 10, 11, 12, 13, 14, 44, 43, 27, 28, 42] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 291 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450615 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450615 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450615/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450615 Building REAL300024450616 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450616' /scratch/stefan/7786230/working/building/REAL300024450616 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450616 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450616/0 /scratch/stefan/7786230/working/building/REAL300024450616 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/488 `/scratch/stefan/7786230/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1) `REAL300024450616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450616/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450616 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 59, 177, 177, 177, 177, 177, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 177, 1, 2, 2, 2, 7, 7] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 313 number of broken/clashed sets: 35 ./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: REAL300024450616 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 177, 177, 177, 177, 177, 168, 67, 168, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 177, 67, 67, 1, 177, 177, 177, 177, 201, 201] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 608 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450616 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 7, 7, 7, 7, 7, 14, 14, 49, 111, 201, 201, 201, 201, 201, 7, 7, 1, 1, 2, 2, 2, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 49, 49, 201, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 421 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450616 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450616 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450616/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450616 Building REAL300024450617 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450617' /scratch/stefan/7786230/working/building/REAL300024450617 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450617 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450617/0 /scratch/stefan/7786230/working/building/REAL300024450617 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/489 `/scratch/stefan/7786230/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CNC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450617/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450617 none CC1C(NC(=O)C2=CNC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 53, 108, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 53, 53, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 440 number of broken/clashed sets: 27 ./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: REAL300024450617 none CC1C(NC(=O)C2=CNC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 134, 134, 134, 201, 201, 201, 201, 201, 201, 117, 117, 117, 113, 53, 113, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 134, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 53, 53, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 560 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450617 none CC1C(NC(=O)C2=CNC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 37, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 117] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 207 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450617 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450617 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450617/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450617 Building REAL300024450618 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450618' /scratch/stefan/7786230/working/building/REAL300024450618 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450618 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450618/0 /scratch/stefan/7786230/working/building/REAL300024450618 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/490 `/scratch/stefan/7786230/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450618/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450618 none CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 171, 63, 63, 63, 51, 51, 51, 51, 51, 49, 26, 49, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 63, 51, 51, 51, 51, 51, 51, 51, 26, 26, 1, 51, 51, 51, 51] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 798 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450618 none CCCCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 27, 31, 27, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 51, 51, 51, 51, 51, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 275 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450618 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450618 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450618/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450618 Building REAL300024450619 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450619' /scratch/stefan/7786230/working/building/REAL300024450619 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450619 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450619/0 /scratch/stefan/7786230/working/building/REAL300024450619 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/491 `/scratch/stefan/7786230/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(F)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450619/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450619 none CC1C(NC(=O)C2(F)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 25, 25, 80, 119, 186, 186, 186, 186, 186, 20, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 80, 80, 186] 186 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 481 number of broken/clashed sets: 31 ./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: REAL300024450619 none CC1C(NC(=O)C2(F)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 93, 93, 93, 112, 112, 112, 186, 186, 186, 186, 186, 186, 93, 93, 93, 86, 39, 86, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 112, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 93, 93, 93, 93, 93, 93, 39, 39, 1] 186 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 594 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450619 none CC1C(NC(=O)C2(F)CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 3, 14, 29, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 14, 14, 93] 186 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450619 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450619 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450619/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450619 Building REAL300024450620 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450620' /scratch/stefan/7786230/working/building/REAL300024450620 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450620 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450620/0 /scratch/stefan/7786230/working/building/REAL300024450620 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/492 `/scratch/stefan/7786230/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450620/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450620 none CC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 97, 93, 97, 97, 90, 71, 71, 71, 55, 55, 55, 55, 55, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 97, 97, 97, 97, 97, 97, 97, 97, 93, 93, 90, 90, 71, 55, 55, 55, 55, 55, 55, 55, 29, 29, 1, 55, 55, 55, 55] 97 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 398 number of broken/clashed sets: 96 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450620 none CC[N@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 16, 14, 16, 16, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 16, 55, 55, 55, 55, 55, 1, 1, 18, 18, 18, 18, 18, 16, 16, 16, 14, 14, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 55, 1, 2, 2, 2] 97 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 166 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450620 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450620/1 /scratch/stefan/7786230/working/building/REAL300024450620 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/493 `/scratch/stefan/7786230/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450620/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450620 none CC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 131, 131, 131, 86, 86, 86, 86, 86, 79, 30, 79, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 131, 86, 86, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86, 86, 86] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 818 number of broken/clashed sets: 200 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450620 none CC[N@@H+](C)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 22, 20, 22, 22, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 86, 86, 86, 86, 86, 1, 1, 26, 26, 26, 26, 26, 22, 22, 22, 20, 20, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450620 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450620 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450620/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450620/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450620 Building REAL300024450621 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450621' /scratch/stefan/7786230/working/building/REAL300024450621 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450621 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450621/0 /scratch/stefan/7786230/working/building/REAL300024450621 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/494 `/scratch/stefan/7786230/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC23CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450621/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450621 none CC1C(NC(=O)C2CC23CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 32, 32, 83, 113, 193, 193, 193, 193, 193, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 83, 83, 193] 193 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 516 number of broken/clashed sets: 36 ./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: REAL300024450621 none CC1C(NC(=O)C2CC23CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 85, 85, 85, 123, 123, 123, 193, 193, 193, 193, 193, 193, 85, 85, 85, 79, 43, 79, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 123, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 85, 85, 85, 85, 85, 85, 43, 43, 1] 193 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 672 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450621 none CC1C(NC(=O)C2CC23CCCC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 14, 22, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 14, 14, 85] 193 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450621 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450621 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450621/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450621 Building REAL300024450622 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450622' /scratch/stefan/7786230/working/building/REAL300024450622 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450622 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450622/0 /scratch/stefan/7786230/working/building/REAL300024450622 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/495 `/scratch/stefan/7786230/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450622/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450622 none CC1=CON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 46, 154, 154, 154, 154, 154, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 154, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 256 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: REAL300024450622 none CC1=CON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 201, 154, 154, 154, 154, 154, 149, 59, 149, 13, 1, 1, 1, 1, 1, 1, 1, 154, 154, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 154, 154, 59, 59, 1, 154, 154, 154, 154] 201 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 614 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450622 none CC1=CON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 50, 106, 201, 201, 201, 201, 201, 9, 9, 2, 2, 2, 1, 3, 9, 9, 9, 9, 9, 9, 9, 50, 50, 201, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 436 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450622 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450622 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450622/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450622 Building REAL300024450623 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450623' /scratch/stefan/7786230/working/building/REAL300024450623 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450623 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450623/0 /scratch/stefan/7786230/working/building/REAL300024450623 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/496 `/scratch/stefan/7786230/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC23CCOC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450623/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450623 none CC1C(NC(=O)C2CC23CCOC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 64, 110, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 64, 64, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 461 number of broken/clashed sets: 35 ./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: REAL300024450623 none CC1C(NC(=O)C2CC23CCOC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [120, 120, 120, 120, 140, 140, 140, 201, 201, 201, 201, 201, 201, 120, 120, 120, 110, 47, 110, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 120, 47, 47, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 670 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450623 none CC1C(NC(=O)C2CC23CCOC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 14, 31, 120, 120, 120, 120, 120, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 14, 14, 120] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450623 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450623 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450623/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450623 Building REAL300024450624 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450624' /scratch/stefan/7786230/working/building/REAL300024450624 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450624 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450624/0 /scratch/stefan/7786230/working/building/REAL300024450624 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/497 `/scratch/stefan/7786230/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450624/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450624 none COCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 151, 151, 125, 66, 125, 66, 66, 51, 51, 51, 51, 51, 50, 26, 50, 12, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 151, 151, 151, 151, 125, 125, 125, 125, 66, 51, 51, 51, 51, 51, 51, 51, 26, 26, 1, 51, 51, 51, 51] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 904 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450624 none COCCCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 28, 15, 15, 9, 3, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 51, 51, 51, 51, 51, 1, 1, 33, 33, 33, 28, 28, 15, 15, 15, 15, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 51, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450624 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450624 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450624/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450624 Building REAL300024450625 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450625' /scratch/stefan/7786230/working/building/REAL300024450625 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450625 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450625/0 /scratch/stefan/7786230/working/building/REAL300024450625 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/498 `/scratch/stefan/7786230/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450625/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450625 none CCC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [188, 200, 139, 200, 201, 201, 201, 139, 139, 119, 119, 119, 119, 119, 107, 31, 107, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 200, 200, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 119, 119, 119, 119, 119, 119, 119, 31, 31, 1, 119, 119, 119, 119] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 810 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450625 none CCC(CC(C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 3, 12, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 31, 119, 119, 119, 119, 119, 1, 1, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 119, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 289 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450625 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450625 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450625/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450625 Building REAL300024450626 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450626' /scratch/stefan/7786230/working/building/REAL300024450626 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450626 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450626/0 /scratch/stefan/7786230/working/building/REAL300024450626 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/499 `/scratch/stefan/7786230/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450626/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450626 none CC(C)CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [194, 194, 194, 194, 165, 194, 194, 165, 165, 126, 126, 126, 126, 126, 111, 31, 111, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 165, 126, 126, 126, 126, 126, 126, 126, 31, 31, 1, 126, 126, 126, 126] 194 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 639 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450626 none CC(C)CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 41, 126, 126, 126, 126, 126, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 126, 1, 2, 2, 2] 194 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 248 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450626 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450626 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450626/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450626 Building REAL300024450627 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450627' /scratch/stefan/7786230/working/building/REAL300024450627 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450627 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450627/0 /scratch/stefan/7786230/working/building/REAL300024450627 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/500 `/scratch/stefan/7786230/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450627/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450627 none CC1C(NC(=O)CCCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 46, 46, 46, 117, 141, 148, 192, 201, 201, 43, 43, 43, 43, 33, 43, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 46, 117, 117, 148, 148, 148, 148, 192, 192, 201, 201, 43, 43, 43, 43, 43, 43, 33, 33, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 936 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450627 none CC1C(NC(=O)CCCCC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 17, 21, 49, 75, 75, 1, 1, 1, 1, 1, 3, 3, 6, 11, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 3, 13, 13, 21, 21, 21, 21, 49, 49, 75, 75, 1, 1, 1, 1, 1, 1, 6, 6, 43] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450627 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450627 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450627/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450627 Building REAL300024450628 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450628' /scratch/stefan/7786230/working/building/REAL300024450628 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450628 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450628/0 /scratch/stefan/7786230/working/building/REAL300024450628 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/501 `/scratch/stefan/7786230/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1=CC=CO1) `REAL300024450628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450628/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450628 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [184, 114, 114, 114, 89, 89, 89, 89, 89, 85, 30, 85, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 184, 201, 201, 201, 201, 184, 184, 184, 184, 114, 89, 89, 89, 89, 89, 89, 89, 30, 30, 1, 89, 89, 89, 89, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 767 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: REAL300024450628 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 29, 29, 38, 38, 38, 38, 38, 56, 56, 96, 131, 201, 201, 201, 201, 201, 38, 38, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 38, 38, 38, 38, 38, 38, 38, 96, 96, 201, 38, 38, 38, 38, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 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]) total number of confs: 562 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450628 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 89, 89, 89, 89, 89, 1, 1, 13, 38, 38, 38, 38, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 89, 1, 2, 2, 2, 38, 38, 38] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 218 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450628 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450628 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450628/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450628 Building REAL300024450629 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450629' /scratch/stefan/7786230/working/building/REAL300024450629 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450629 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450629/0 /scratch/stefan/7786230/working/building/REAL300024450629 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/502 `/scratch/stefan/7786230/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450629/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450629 none CC1C(NC(=O)C2(C)CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 49, 105, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 5, 2, 2, 2, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 49, 49, 201] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 445 number of broken/clashed sets: 18 ./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: REAL300024450629 none CC1C(NC(=O)C2(C)CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [142, 142, 142, 142, 163, 163, 163, 201, 201, 201, 201, 201, 201, 142, 142, 142, 138, 56, 138, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 163, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 142, 56, 56, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 635 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450629 none CC1C(NC(=O)C2(C)CCNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 12, 43, 142, 142, 142, 142, 142, 2, 2, 2, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 142] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450629 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450629 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450629/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450629 Building REAL300024450630 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450630' /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450630 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450630/0 /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/503 `/scratch/stefan/7786230/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450630/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 28, 21, 28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 22, 84, 84, 84, 84, 84, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 84, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 47, 41, 10, 11, 12, 13, 14, 44, 16, 27, 51, 46, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 239 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: REAL300024450630 none CC1CCC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 198, 201, 131, 131, 131, 84, 84, 84, 84, 84, 76, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 131, 84, 84, 84, 84, 84, 84, 84, 30, 30, 1, 84, 84, 84, 84] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 773 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 12, 12, 12, 28, 28, 28, 28, 28, 44, 44, 106, 149, 201, 201, 201, 201, 201, 28, 28, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 28, 28, 28, 28, 28, 28, 28, 106, 106, 201, 28, 28, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 599 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450630/1 /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/504 `/scratch/stefan/7786230/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450630.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450630/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 24, 24, 24, 24, 24, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 1, 2, 2, 2] 27 rigid atoms, others: [45, 43, 47, 41, 10, 11, 12, 13, 14, 44, 16, 27, 51, 46, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 27 ./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: REAL300024450630 none CC1CCC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 24, 23, 17, 23, 11, 1, 1, 1, 1, 1, 1, 1, 24, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 24, 24, 24, 17, 17, 1, 24, 24, 24, 24] 27 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 2, 6, 6, 6, 8, 8, 8, 8, 8, 9, 9, 16, 21, 27, 27, 27, 27, 27, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 8, 8, 8, 8, 8, 8, 8, 16, 16, 27, 8, 8, 8, 8] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450630/2 /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/505 `/scratch/stefan/7786230/working/3D/505' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450630.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450630/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 20, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 102, 102, 102, 102, 102, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 102, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 221 number of broken/clashed sets: 24 ./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: REAL300024450630 none CC1CCCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 199, 118, 118, 118, 102, 102, 102, 102, 102, 92, 29, 92, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 118, 102, 102, 102, 102, 102, 102, 102, 29, 29, 1, 102, 102, 102, 102] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 736 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450630 none CC1CCCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 16, 16, 16, 20, 20, 20, 20, 20, 33, 33, 85, 121, 201, 201, 201, 201, 201, 20, 20, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 20, 20, 20, 20, 20, 20, 20, 85, 85, 201, 20, 20, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 539 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450630 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450630 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450630/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450630/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450630/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450630 Building REAL300024450631 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450631' /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450631 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450631/0 /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/506 `/scratch/stefan/7786230/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450631/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CC[N@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 40, 40, 21, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 81, 81, 81, 81, 81, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 81, 1, 2, 2, 2, 40, 40] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52, 53, 54]) total number of confs: 267 number of broken/clashed sets: 20 ./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: REAL300024450631 none CC1CC[N@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 182, 201, 128, 128, 128, 81, 81, 81, 81, 81, 74, 30, 74, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 128, 81, 81, 81, 81, 81, 81, 81, 30, 30, 1, 81, 81, 81, 81, 201, 201] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 779 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CC[N@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 22, 22, 22, 40, 40, 40, 40, 40, 58, 58, 105, 146, 201, 201, 201, 201, 201, 40, 40, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 22, 40, 40, 40, 40, 40, 40, 40, 105, 105, 201, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 580 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450631/1 /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/507 `/scratch/stefan/7786230/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450631.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450631/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CC[N@@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 19, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 80, 80, 80, 80, 80, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 80, 1, 2, 2, 2, 34, 34] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52, 53, 54]) total number of confs: 249 number of broken/clashed sets: 23 ./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: REAL300024450631 none CC1CC[N@@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 190, 201, 125, 125, 125, 80, 80, 80, 80, 80, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 125, 80, 80, 80, 80, 80, 80, 80, 29, 29, 1, 80, 80, 80, 80, 201, 201] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 765 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CC[N@@H+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 18, 18, 18, 34, 34, 34, 34, 34, 54, 54, 104, 142, 201, 201, 201, 201, 201, 34, 34, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 18, 34, 34, 34, 34, 34, 34, 34, 104, 104, 201, 34, 34, 34, 34, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 595 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450631/2 /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/508 `/scratch/stefan/7786230/working/3D/508' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450631.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450631/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CCN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 26, 26, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 77, 77, 77, 77, 77, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 77, 1, 2, 2, 2, 26, 26] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51, 52, 53]) total number of confs: 202 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: REAL300024450631 none CC1CCN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 198, 92, 92, 92, 77, 77, 77, 77, 77, 74, 29, 74, 12, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 92, 77, 77, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77, 77, 77, 201, 201] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 746 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450631 none CC1CCN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 19, 19, 19, 26, 26, 26, 26, 26, 38, 38, 81, 118, 201, 201, 201, 201, 201, 26, 26, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 19, 26, 26, 26, 26, 26, 26, 26, 81, 81, 201, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 52, 53, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 543 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450631 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450631 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450631/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450631/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450631/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450631 Building REAL300024450632 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450632' /scratch/stefan/7786230/working/building/REAL300024450632 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450632 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450632/0 /scratch/stefan/7786230/working/building/REAL300024450632 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/509 `/scratch/stefan/7786230/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2C[C@H]2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450632/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450632 none CC1C(NC(=O)[C@H]2C[C@H]2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 27, 27, 70, 107, 194, 194, 194, 194, 194, 17, 17, 17, 17, 17, 7, 1, 1, 7, 7, 17, 17, 17, 17, 17, 17, 70, 70, 194] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 495 number of broken/clashed sets: 33 ./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: REAL300024450632 none CC1C(NC(=O)[C@H]2C[C@H]2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 93, 93, 93, 139, 139, 139, 194, 194, 194, 194, 194, 201, 201, 93, 93, 93, 90, 39, 90, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 139, 194, 194, 201, 201, 93, 93, 93, 93, 93, 93, 39, 39, 1] 201 rigid atoms, others: [46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 684 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450632 none CC1C(NC(=O)[C@H]2C[C@H]2C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 17, 17, 17, 17, 17, 29, 29, 1, 1, 1, 1, 1, 3, 3, 12, 25, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 6, 17, 17, 29, 29, 1, 1, 1, 1, 1, 1, 12, 12, 93] 201 rigid atoms, others: [0, 1, 2, 3, 38, 32, 40, 41, 42, 39, 14, 15, 16, 17, 18, 43, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450632 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450632 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450632/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450632 Building REAL300024450633 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450633' /scratch/stefan/7786230/working/building/REAL300024450633 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450633 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450633/0 /scratch/stefan/7786230/working/building/REAL300024450633 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/510 `/scratch/stefan/7786230/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450633/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450633 none CC[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [134, 138, 97, 138, 97, 97, 43, 43, 43, 43, 43, 43, 30, 43, 12, 1, 1, 1, 1, 1, 1, 1, 43, 43, 138, 138, 138, 138, 138, 138, 138, 138, 138, 97, 43, 43, 43, 43, 43, 43, 43, 30, 30, 1, 43, 43, 43, 43, 138, 138, 138, 138, 138, 138] 138 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 547 number of broken/clashed sets: 127 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450633 none CC[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [25, 24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 43, 43, 43, 43, 43, 1, 1, 24, 27, 27, 27, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 1, 2, 2, 2, 27, 27, 27, 27, 27, 27] 138 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 238 number of broken/clashed sets: 127 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450633 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450633 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450633/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450633 Building REAL300024450634 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450634' /scratch/stefan/7786230/working/building/REAL300024450634 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450634 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450634/0 /scratch/stefan/7786230/working/building/REAL300024450634 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/511 `/scratch/stefan/7786230/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(F)F) `REAL300024450634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450634/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450634 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [111, 87, 87, 87, 58, 58, 58, 58, 58, 56, 40, 56, 12, 1, 1, 1, 1, 1, 1, 1, 58, 58, 111, 108, 116, 116, 111, 111, 111, 111, 87, 58, 58, 58, 58, 58, 58, 58, 40, 40, 1, 58, 58, 58, 58, 116, 116, 116] 116 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 494 number of broken/clashed sets: 46 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450634 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 58, 58, 58, 58, 58, 1, 1, 18, 21, 24, 24, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 1, 2, 2, 2, 24, 24, 24] 116 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450634 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450634 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450634/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450634 Building REAL300024450635 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450635' /scratch/stefan/7786230/working/building/REAL300024450635 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450635 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450635/0 /scratch/stefan/7786230/working/building/REAL300024450635 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/512 `/scratch/stefan/7786230/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450635/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450635 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 10, 19, 19, 19, 19, 19, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 1, 2, 2, 2, 5] 23 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 60 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: REAL300024450635 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 18, 16, 18, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 23, 23, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 1, 19, 19, 19, 19, 23] 23 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450635 none CC1=NC(C)=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 8, 8, 14, 17, 23, 23, 23, 23, 23, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 23, 5, 5, 5, 5, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450635 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450635 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450635/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450635 Building REAL300024450636 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450636' /scratch/stefan/7786230/working/building/REAL300024450636 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450636 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450636/0 /scratch/stefan/7786230/working/building/REAL300024450636 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/513 `/scratch/stefan/7786230/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1) `REAL300024450636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450636/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450636 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 84, 84, 84, 84, 84, 1, 1, 29, 29, 29, 29, 29, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 84, 1, 2, 2, 2, 29, 29] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 207 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: REAL300024450636 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 106, 106, 106, 84, 84, 84, 84, 84, 81, 31, 81, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 197, 197, 106, 84, 84, 84, 84, 84, 84, 84, 31, 31, 1, 84, 84, 84, 84, 201, 201] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 799 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450636 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 21, 21, 21, 29, 29, 29, 29, 29, 45, 45, 84, 120, 201, 201, 201, 201, 201, 29, 29, 1, 1, 2, 2, 2, 7, 7, 21, 29, 29, 29, 29, 29, 29, 29, 84, 84, 201, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 48, 25, 26] set([5, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450636 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450636 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450636/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450636 Building REAL300024450637 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450637' /scratch/stefan/7786230/working/building/REAL300024450637 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450637 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450637/0 /scratch/stefan/7786230/working/building/REAL300024450637 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/514 `/scratch/stefan/7786230/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450637/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450637 none CC1C(NC(=O)CCC2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 35, 35, 12, 35, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 46, 46, 93, 131, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 35, 12, 12, 6, 6, 1, 1, 40, 40, 40, 40, 40, 40, 93, 93, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 585 number of broken/clashed sets: 33 ./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: REAL300024450637 none CC1C(NC(=O)CCC2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 62, 62, 62, 167, 198, 201, 201, 201, 201, 44, 44, 44, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 62, 167, 167, 198, 198, 201, 201, 44, 44, 44, 44, 44, 44, 28, 28, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 805 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450637 none CC1C(NC(=O)CCC2=NNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 21, 40, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 8, 13, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 4, 15, 15, 21, 21, 40, 40, 1, 1, 1, 1, 1, 1, 8, 8, 44] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450637 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450637/1 /scratch/stefan/7786230/working/building/REAL300024450637 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/515 `/scratch/stefan/7786230/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=CNN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450637.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450637/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450637 none CC1C(NC(=O)CCC2=CNN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 32, 32, 11, 32, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 41, 41, 85, 126, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 32, 11, 11, 6, 6, 1, 1, 35, 35, 35, 35, 35, 35, 85, 85, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 547 number of broken/clashed sets: 35 ./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: REAL300024450637 none CC1C(NC(=O)CCC2=CNN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 65, 65, 65, 84, 84, 84, 170, 186, 201, 201, 201, 201, 65, 65, 65, 63, 35, 63, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 84, 170, 170, 186, 186, 201, 201, 65, 65, 65, 65, 65, 65, 35, 35, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 774 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450637 none CC1C(NC(=O)CCC2=CNN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 21, 35, 35, 35, 35, 1, 1, 1, 1, 1, 3, 3, 12, 21, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 4, 15, 15, 21, 21, 35, 35, 1, 1, 1, 1, 1, 1, 12, 12, 65] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450637 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450637 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450637/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450637/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450637 Building REAL300024450638 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450638' /scratch/stefan/7786230/working/building/REAL300024450638 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450638 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450638/0 /scratch/stefan/7786230/working/building/REAL300024450638 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/516 `/scratch/stefan/7786230/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CF)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450638/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450638 none CC1C(NC(=O)C2(CF)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [34, 35, 4, 37, 6, 7, 9, 10, 11, 36, 38, 39] set([0, 1, 2, 3, 5, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 16 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: REAL300024450638 none CC1C(NC(=O)C2(CF)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450638 none CC1C(NC(=O)C2(CF)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450638 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450638 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450638/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450638 Building REAL300024450639 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450639' /scratch/stefan/7786230/working/building/REAL300024450639 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450639 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450639/0 /scratch/stefan/7786230/working/building/REAL300024450639 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/517 `/scratch/stefan/7786230/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450639/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450639 none C=C[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 12, 12, 12, 12, 12, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 99, 99, 99, 99, 99, 1, 1, 26, 26, 26, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 99, 1, 2, 2, 2] 201 rigid atoms, others: [43, 47, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 23 ./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: REAL300024450639 none C=C[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 113, 201, 113, 113, 98, 98, 98, 98, 98, 87, 28, 87, 12, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 113, 98, 98, 98, 98, 98, 98, 98, 28, 28, 1, 98, 98, 98, 98] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 634 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450639 none C=C[C@@H]1OCC[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 12, 12, 19, 19, 60, 103, 201, 201, 201, 201, 201, 12, 12, 5, 5, 5, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 60, 60, 201, 12, 12, 12, 12] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 461 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450639 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450639 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450639/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450639 Building REAL300024450640 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450640' /scratch/stefan/7786230/working/building/REAL300024450640 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450640 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450640/0 /scratch/stefan/7786230/working/building/REAL300024450640 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/518 `/scratch/stefan/7786230/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450640/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450640 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 19, 19, 19, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 46, 46, 46, 46, 46, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 47, 41, 42, 11, 12, 13, 14, 15, 16, 17, 51, 46, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 227 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: REAL300024450640 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 150, 150, 150, 58, 150, 58, 58, 46, 46, 46, 46, 46, 45, 23, 45, 12, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 58, 46, 46, 46, 46, 46, 46, 46, 23, 23, 1, 46, 46, 46, 46] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 740 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450640 none CC(C)C[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 19, 19, 19, 32, 32, 50, 79, 150, 150, 150, 150, 150, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 12, 19, 19, 19, 19, 19, 19, 19, 50, 50, 150, 19, 19, 19, 19] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 9, 39, 6] set([0, 1, 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, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450640 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450640 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450640/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450640 Building REAL300024450641 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450641' /scratch/stefan/7786230/working/building/REAL300024450641 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450641 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450641/0 /scratch/stefan/7786230/working/building/REAL300024450641 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/519 `/scratch/stefan/7786230/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450641/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450641 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 46, 46, 85, 123, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 22, 8, 8, 1, 1, 30, 30, 30, 30, 30, 30, 85, 85, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 6 ./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: REAL300024450641 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 92, 116, 116, 116, 195, 201, 201, 201, 201, 92, 92, 92, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 116, 195, 195, 201, 201, 92, 92, 92, 92, 92, 92, 30, 30, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 754 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450641 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 17, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 4, 18, 18, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 92] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450641 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450641 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450641/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450641 Building REAL300024450642 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450642' /scratch/stefan/7786230/working/building/REAL300024450642 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450642 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450642/0 /scratch/stefan/7786230/working/building/REAL300024450642 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/520 `/scratch/stefan/7786230/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C2CC2)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450642/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450642 none CC1C(NC(=O)C(C2CC2)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 38] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 13 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.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: REAL300024450642 none CC1C(NC(=O)C(C2CC2)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 1] 4 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 8 number of broken/clashed sets: 0 ./output.4.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: REAL300024450642 none CC1C(NC(=O)C(C2CC2)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 4, 1, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [43, 6, 39, 40, 41, 10, 11, 12, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 13 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450642 none CC1C(NC(=O)C(C2CC2)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3] 4 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450642 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450642 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450642/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450642 Building REAL300024450643 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450643' /scratch/stefan/7786230/working/building/REAL300024450643 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450643 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450643/0 /scratch/stefan/7786230/working/building/REAL300024450643 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/521 `/scratch/stefan/7786230/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450643/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450643 none CC1C(NC(=O)CC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 25, 25, 40, 55, 89, 89, 89, 89, 89, 21, 21, 21, 21, 21, 19, 7, 7, 1, 1, 21, 21, 21, 21, 21, 21, 40, 40, 89] 89 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 254 number of broken/clashed sets: 10 ./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: REAL300024450643 none CC1C(NC(=O)CC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 66, 66, 66, 82, 89, 89, 89, 89, 62, 62, 62, 62, 25, 62, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 66, 82, 82, 89, 89, 62, 62, 62, 62, 62, 62, 25, 25, 1] 89 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 307 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450643 none CC1C(NC(=O)CC2=NNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 11, 20, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 3, 7, 7, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 62] 89 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450643 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450643/1 /scratch/stefan/7786230/working/building/REAL300024450643 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/522 `/scratch/stefan/7786230/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450643.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450643/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450643 none CC1C(NC(=O)CC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 20, 20, 6, 20, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50, 50, 98, 136, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 20, 6, 6, 1, 1, 32, 32, 32, 32, 32, 32, 98, 98, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 580 number of broken/clashed sets: 9 ./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: REAL300024450643 none CC1C(NC(=O)CC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 81, 81, 125, 125, 125, 201, 201, 201, 201, 201, 81, 81, 81, 77, 29, 77, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 125, 201, 201, 201, 201, 81, 81, 81, 81, 81, 81, 29, 29, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 802 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450643 none CC1C(NC(=O)CC2=NN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 21, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 4, 20, 20, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 81] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450643 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450643 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450643/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450643/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450643 Building REAL300024450644 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450644' /scratch/stefan/7786230/working/building/REAL300024450644 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450644 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450644/0 /scratch/stefan/7786230/working/building/REAL300024450644 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/523 `/scratch/stefan/7786230/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCC1) `REAL300024450644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450644/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450644 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 121, 121, 108, 108, 108, 108, 108, 95, 31, 95, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 108, 108, 108, 108, 108, 108, 108, 31, 31, 1, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 777 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: REAL300024450644 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 10, 10, 10, 16, 16, 16, 16, 16, 27, 27, 81, 123, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 16, 16, 16, 16, 16, 16, 16, 81, 81, 201, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 46, 47, 48, 49, 50, 51, 52, 53, 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]) total number of confs: 523 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450644 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 28, 108, 108, 108, 108, 108, 1, 1, 12, 16, 16, 16, 16, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 108, 1, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 229 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450644 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450644 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450644/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450644 Building REAL300024450645 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450645' /scratch/stefan/7786230/working/building/REAL300024450645 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450645 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450645/0 /scratch/stefan/7786230/working/building/REAL300024450645 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/524 `/scratch/stefan/7786230/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450645/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450645 none CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 190, 90, 90, 90, 71, 71, 71, 71, 71, 69, 37, 69, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 90, 71, 71, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71, 71, 71, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] 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, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 883 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450645 none CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 13, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 71, 71, 71, 71, 71, 1, 1, 10, 16, 16, 15, 15, 15, 15, 15, 13, 13, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 1, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 46, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 215 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450645 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450645 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450645/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450645 Building REAL300024450646 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450646' /scratch/stefan/7786230/working/building/REAL300024450646 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450646 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450646/0 /scratch/stefan/7786230/working/building/REAL300024450646 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/525 `/scratch/stefan/7786230/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450646/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450646 none CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6] 7 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 16 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450646 none CC(C)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 1, 2, 2, 2] 7 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450646 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450646 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450646/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450646 Building REAL300024450647 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450647' /scratch/stefan/7786230/working/building/REAL300024450647 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450647 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450647/0 /scratch/stefan/7786230/working/building/REAL300024450647 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/526 `/scratch/stefan/7786230/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450647/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450647 none CC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 22, 22, 22, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 66, 66, 66, 66, 66, 1, 1, 36, 36, 36, 36, 36, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 66, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 251 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: REAL300024450647 none CC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 201, 81, 81, 66, 66, 66, 66, 66, 62, 36, 62, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 81, 66, 66, 66, 66, 66, 66, 66, 36, 36, 1, 66, 66, 66, 66] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 620 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450647 none CC[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 22, 22, 22, 22, 22, 32, 32, 72, 104, 201, 201, 201, 201, 201, 22, 22, 3, 3, 3, 3, 3, 1, 1, 12, 22, 22, 22, 22, 22, 22, 22, 72, 72, 201, 22, 22, 22, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450647 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450647 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450647/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450647 Building REAL300024450648 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450648' /scratch/stefan/7786230/working/building/REAL300024450648 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450648 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450648/0 /scratch/stefan/7786230/working/building/REAL300024450648 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/527 `/scratch/stefan/7786230/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450648/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450648 none CC1C(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 62, 87, 141, 141, 141, 141, 141, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 62, 62, 141] 141 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 374 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: REAL300024450648 none CC1C(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 92, 92, 92, 141, 141, 141, 141, 141, 141, 141, 141, 141, 76, 76, 76, 71, 39, 71, 12, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 92, 141, 141, 141, 141, 141, 141, 76, 76, 76, 76, 76, 76, 39, 39, 1] 141 rigid atoms, others: [50, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 460 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450648 none CC1C(NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 14, 27, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 14, 14, 76] 141 rigid atoms, others: [0, 1, 2, 3, 33, 42, 43, 44, 34, 46, 45, 16, 17, 18, 19, 20, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450648 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450648 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450648/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450648 Building REAL300024450649 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450649' /scratch/stefan/7786230/working/building/REAL300024450649 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450649 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450649/0 /scratch/stefan/7786230/working/building/REAL300024450649 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/528 `/scratch/stefan/7786230/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(C)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450649/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450649 none CCC(NC(C)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [184, 190, 86, 190, 201, 201, 201, 86, 86, 73, 73, 73, 73, 73, 71, 28, 71, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 190, 201, 201, 201, 201, 86, 73, 73, 73, 73, 73, 73, 73, 28, 28, 1, 73, 73, 73, 73] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 934 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450649 none CCC(NC(C)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 14, 3, 14, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 73, 73, 73, 73, 73, 1, 1, 22, 22, 22, 22, 22, 14, 22, 22, 22, 22, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 73, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450649 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450649 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450649/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450649 Building REAL300024450650 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450650' /scratch/stefan/7786230/working/building/REAL300024450650 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450650 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450650/0 /scratch/stefan/7786230/working/building/REAL300024450650 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/529 `/scratch/stefan/7786230/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450650/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450650 none CC(C)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 165, 164, 189, 57, 57, 57, 44, 44, 44, 44, 44, 41, 23, 41, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 201, 201, 200, 201, 201, 201, 201, 201, 201, 200, 200, 189, 189, 57, 44, 44, 44, 44, 44, 44, 44, 23, 23, 1, 44, 44, 44, 44] 201 rigid atoms, others: [49, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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, 50, 51, 52, 53]) total number of confs: 1248 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450650 none CC(C)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 26, 24, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 44, 44, 44, 44, 44, 1, 1, 32, 32, 31, 32, 32, 32, 32, 31, 31, 30, 30, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 44, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 8, 9, 10, 11, 12, 13, 46, 44, 40, 50, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 301 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450650 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450650 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450650/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450650 Building REAL300024450651 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450651' /scratch/stefan/7786230/working/building/REAL300024450651 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450651 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450651/0 /scratch/stefan/7786230/working/building/REAL300024450651 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/530 `/scratch/stefan/7786230/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450651/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450651 none CC1C(NC(=O)C2CC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 1, 11, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 26, 26, 58, 102, 201, 201, 201, 201, 201, 18, 18, 18, 18, 18, 11, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 58, 58, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 465 number of broken/clashed sets: 23 ./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: REAL300024450651 none CC1C(NC(=O)C2CC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 74, 74, 74, 201, 201, 201, 201, 70, 70, 70, 69, 41, 69, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 74, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 41, 41, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 602 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450651 none CC1C(NC(=O)C2CC23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 10, 21, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 3, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 10, 10, 70] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450651 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450651 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450651/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450651 Building REAL300024450652 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450652' /scratch/stefan/7786230/working/building/REAL300024450652 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450652 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450652/0 /scratch/stefan/7786230/working/building/REAL300024450652 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/531 `/scratch/stefan/7786230/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450652/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450652 none CC1C(NC(=O)CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 24, 24, 8, 24, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 39, 39, 74, 118, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 24, 8, 8, 1, 1, 1, 29, 29, 29, 29, 29, 29, 74, 74, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 521 number of broken/clashed sets: 14 ./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: REAL300024450652 none CC1C(NC(=O)CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [109, 109, 109, 109, 123, 123, 123, 187, 201, 201, 201, 201, 109, 109, 109, 102, 29, 102, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 123, 187, 187, 201, 201, 201, 109, 109, 109, 109, 109, 109, 29, 29, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 684 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450652 none CC1C(NC(=O)CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 13, 25, 109, 109, 109, 109, 109, 2, 2, 2, 1, 1, 4, 15, 15, 29, 29, 29, 1, 1, 1, 1, 1, 1, 13, 13, 109] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450652 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450652/1 /scratch/stefan/7786230/working/building/REAL300024450652 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/532 `/scratch/stefan/7786230/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450652.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450652/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450652 none CC1C(NC(=O)CC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 26, 26, 4, 26, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 50, 50, 93, 130, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 26, 4, 4, 1, 1, 1, 33, 33, 33, 33, 33, 33, 93, 93, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 563 number of broken/clashed sets: 7 ./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: REAL300024450652 none CC1C(NC(=O)CC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [63, 63, 63, 63, 79, 79, 79, 193, 201, 201, 201, 201, 63, 63, 63, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 79, 193, 193, 201, 201, 201, 63, 63, 63, 63, 63, 63, 26, 26, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 736 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450652 none CC1C(NC(=O)CC2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 20, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 10, 17, 63, 63, 63, 63, 63, 2, 2, 2, 1, 1, 3, 20, 20, 33, 33, 33, 1, 1, 1, 1, 1, 1, 10, 10, 63] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450652 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450652 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450652/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450652/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450652 Building REAL300024450653 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450653' /scratch/stefan/7786230/working/building/REAL300024450653 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450653 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450653/0 /scratch/stefan/7786230/working/building/REAL300024450653 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/533 `/scratch/stefan/7786230/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1C) `REAL300024450653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450653/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450653 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 70, 70, 70, 70, 70, 1, 1, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 70, 1, 2, 2, 2, 9, 9, 9] 92 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 18 ./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: REAL300024450653 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 84, 84, 84, 70, 70, 70, 70, 70, 66, 35, 66, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 92, 92, 92, 92, 92, 92, 92, 84, 70, 70, 70, 70, 70, 70, 70, 35, 35, 1, 70, 70, 70, 70, 92, 92, 92] 92 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 296 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450653 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 12, 12, 36, 54, 92, 92, 92, 92, 92, 9, 9, 1, 1, 1, 2, 2, 2, 1, 4, 9, 9, 9, 9, 9, 9, 9, 36, 36, 92, 9, 9, 9, 9, 2, 2, 2] 92 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450653 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450653 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450653/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450653 Building REAL300024450654 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450654' /scratch/stefan/7786230/working/building/REAL300024450654 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450654 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450654/0 /scratch/stefan/7786230/working/building/REAL300024450654 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/534 `/scratch/stefan/7786230/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1) `REAL300024450654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450654/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450654 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 38, 109, 109, 109, 109, 109, 1, 1, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 109, 1, 2, 2, 2, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 31 ./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: REAL300024450654 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 115, 115, 109, 109, 109, 109, 109, 107, 54, 107, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 115, 109, 109, 109, 109, 109, 109, 109, 54, 54, 1, 109, 109, 109, 109, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46]) total number of confs: 497 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450654 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 8, 8, 8, 8, 8, 14, 14, 47, 97, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 2, 2, 2, 1, 5, 8, 8, 8, 8, 8, 8, 8, 47, 47, 201, 8, 8, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 430 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450654 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450654 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450654/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450654 Building REAL300024450655 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450655' /scratch/stefan/7786230/working/building/REAL300024450655 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450655 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450655/0 /scratch/stefan/7786230/working/building/REAL300024450655 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/535 `/scratch/stefan/7786230/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450655/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450655 none CC1C(NC(=O)[C@@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 23, 23, 63, 118, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 11, 1, 1, 1, 16, 16, 16, 16, 16, 16, 63, 63, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 474 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: REAL300024450655 none CC1C(NC(=O)[C@@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 152, 152, 152, 201, 201, 201, 201, 201, 117, 117, 117, 112, 50, 112, 12, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 152, 201, 201, 201, 117, 117, 117, 117, 117, 117, 50, 50, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 649 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450655 none CC1C(NC(=O)[C@@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 12, 37, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 4, 16, 16, 16, 1, 1, 1, 1, 1, 1, 12, 12, 117] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450655 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450655 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450655/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450655 Building REAL300024450656 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450656' /scratch/stefan/7786230/working/building/REAL300024450656 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450656 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450656/0 /scratch/stefan/7786230/working/building/REAL300024450656 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/536 `/scratch/stefan/7786230/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450656/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450656 none CC1C(NC(=O)C2(C)CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 63, 120, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 63, 63, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 483 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: REAL300024450656 none CC1C(NC(=O)C2(C)CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [131, 131, 131, 131, 144, 144, 144, 201, 201, 201, 201, 201, 131, 131, 131, 125, 50, 125, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 131, 50, 50, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 631 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450656 none CC1C(NC(=O)C2(C)CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 13, 40, 131, 131, 131, 131, 131, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 131] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450656 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450656 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450656/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450656 Building REAL300024450657 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450657' /scratch/stefan/7786230/working/building/REAL300024450657 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450657 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450657/0 /scratch/stefan/7786230/working/building/REAL300024450657 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/537 `/scratch/stefan/7786230/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450657/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450657 none CC1C(NC(=O)C2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 18, 18, 65, 100, 152, 152, 152, 152, 152, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 65, 65, 152] 152 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 383 number of broken/clashed sets: 29 ./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: REAL300024450657 none CC1C(NC(=O)C2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 101, 101, 101, 152, 152, 152, 152, 152, 100, 100, 100, 93, 42, 93, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 101, 152, 152, 152, 152, 152, 152, 152, 152, 152, 100, 100, 100, 100, 100, 100, 42, 42, 1] 152 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 405 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450657 none CC1C(NC(=O)C2=CCCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 14, 29, 100, 100, 100, 100, 100, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 14, 14, 100] 152 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450657 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450657 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450657/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450657 Building REAL300024450658 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450658' /scratch/stefan/7786230/working/building/REAL300024450658 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450658 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450658/0 /scratch/stefan/7786230/working/building/REAL300024450658 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/538 `/scratch/stefan/7786230/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450658/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450658 none CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 128, 128, 128, 94, 94, 94, 94, 94, 91, 29, 91, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201, 201, 201, 201, 201, 201, 201, 128, 94, 94, 94, 94, 94, 94, 94, 29, 29, 1, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 649 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450658 none CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 94, 94, 94, 94, 94, 1, 1, 16, 24, 24, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 94, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450658 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450658 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450658/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450658 Building REAL300024450659 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450659' /scratch/stefan/7786230/working/building/REAL300024450659 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450659 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450659/0 /scratch/stefan/7786230/working/building/REAL300024450659 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/539 `/scratch/stefan/7786230/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450659/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450659 none CC(C)OC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 171, 201, 201, 171, 171, 106, 106, 106, 106, 106, 98, 27, 98, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 106, 106, 106, 106, 106, 106, 106, 27, 27, 1, 106, 106, 106, 106] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 665 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450659 none CC(C)OC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 106, 106, 106, 106, 106, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 106, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450659 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450659 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450659/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450659 Building REAL300024450660 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450660' /scratch/stefan/7786230/working/building/REAL300024450660 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450660 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450660/0 /scratch/stefan/7786230/working/building/REAL300024450660 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/540 `/scratch/stefan/7786230/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450660/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450660 none CC1C(NC(=O)C2(C)CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 40, 53, 97, 97, 97, 97, 97, 8, 8, 8, 8, 8, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 40, 40, 97] 97 rigid atoms, others: [11, 4, 37, 6, 7, 8, 9, 10, 39, 12, 40, 43, 41, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 20 ./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: REAL300024450660 none CC1C(NC(=O)C2(C)CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 85, 85, 85, 96, 96, 96, 97, 97, 97, 97, 97, 97, 85, 85, 85, 79, 41, 79, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 96, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 85, 85, 85, 85, 85, 85, 41, 41, 1] 97 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 322 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450660 none CC1C(NC(=O)C2(C)CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 16, 26, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 16, 16, 85] 97 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450660 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450660 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450660/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450660 Building REAL300024450661 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450661' /scratch/stefan/7786230/working/building/REAL300024450661 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450661 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450661/0 /scratch/stefan/7786230/working/building/REAL300024450661 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/541 `/scratch/stefan/7786230/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450661/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450661 none CCC(CC)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [116, 109, 85, 109, 117, 109, 121, 85, 85, 61, 61, 61, 61, 61, 59, 46, 59, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 116, 116, 116, 116, 116, 117, 117, 117, 117, 117, 121, 121, 363, 85, 61, 61, 61, 61, 61, 61, 61, 46, 46, 1, 61, 61, 61, 61] 363 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 919 number of broken/clashed sets: 174 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450661 none CCC(CC)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 6, 11, 17, 11, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 61, 61, 61, 61, 61, 1, 1, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 23, 23, 69, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 1, 2, 2, 2] 363 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 342 number of broken/clashed sets: 174 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450661 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450661 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450661/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450661 Building REAL300024450662 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450662' /scratch/stefan/7786230/working/building/REAL300024450662 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450662 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450662/0 /scratch/stefan/7786230/working/building/REAL300024450662 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/542 `/scratch/stefan/7786230/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450662/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450662 none CC1C(NC(=O)C2CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 34, 34, 84, 117, 190, 190, 190, 190, 190, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 84, 84, 190] 190 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 522 number of broken/clashed sets: 36 ./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: REAL300024450662 none CC1C(NC(=O)C2CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 105, 105, 105, 190, 190, 190, 190, 190, 66, 66, 66, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 105, 190, 190, 190, 190, 190, 190, 190, 190, 190, 66, 66, 66, 66, 66, 66, 38, 38, 1] 190 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 633 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450662 none CC1C(NC(=O)C2CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 3, 3, 12, 20, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 12, 12, 66] 190 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450662 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450662 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450662/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450662 Building REAL300024450663 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450663' /scratch/stefan/7786230/working/building/REAL300024450663 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450663 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450663/0 /scratch/stefan/7786230/working/building/REAL300024450663 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/543 `/scratch/stefan/7786230/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450663/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450663 none CC1C(NC(=O)[C@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 24, 24, 65, 116, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 17, 17, 17, 17, 17, 17, 65, 65, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43]) total number of confs: 489 number of broken/clashed sets: 14 ./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: REAL300024450663 none CC1C(NC(=O)[C@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 104, 104, 140, 140, 140, 201, 201, 201, 201, 201, 104, 104, 104, 101, 50, 101, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 140, 201, 201, 201, 104, 104, 104, 104, 104, 104, 50, 50, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 659 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450663 none CC1C(NC(=O)[C@H]2CC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 12, 33, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 4, 17, 17, 17, 1, 1, 1, 1, 1, 1, 12, 12, 104] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450663 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450663 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450663/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450663 Building REAL300024450664 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450664' /scratch/stefan/7786230/working/building/REAL300024450664 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450664 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450664/0 /scratch/stefan/7786230/working/building/REAL300024450664 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/544 `/scratch/stefan/7786230/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450664/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450664 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 46, 46, 85, 123, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 22, 8, 8, 1, 1, 30, 30, 30, 30, 30, 30, 85, 85, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 6 ./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: REAL300024450664 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 92, 116, 116, 116, 195, 201, 201, 201, 201, 92, 92, 92, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 116, 195, 195, 201, 201, 92, 92, 92, 92, 92, 92, 30, 30, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 754 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450664 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 17, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 4, 18, 18, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 92] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450664 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450664 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450664/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450664 Building REAL300024450665 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450665' /scratch/stefan/7786230/working/building/REAL300024450665 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450665 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450665/0 /scratch/stefan/7786230/working/building/REAL300024450665 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/545 `/scratch/stefan/7786230/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450665/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450665 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 49, 49, 49, 49, 49, 1, 1, 34, 34, 36, 36, 36, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 49, 1, 2, 2, 2, 34, 34, 34, 34] 181 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 76 ./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: REAL300024450665 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 100, 100, 100, 49, 49, 49, 49, 49, 47, 36, 47, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 181, 181, 181, 181, 181, 100, 49, 49, 49, 49, 49, 49, 49, 36, 36, 1, 49, 49, 49, 49, 181, 181, 181, 181] 181 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 585 number of broken/clashed sets: 76 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450665 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 34, 51, 51, 102, 137, 181, 181, 181, 181, 181, 34, 34, 1, 1, 4, 4, 4, 10, 34, 34, 34, 34, 34, 34, 34, 102, 102, 181, 34, 34, 34, 34, 1, 1, 1, 1] 181 rigid atoms, others: [1, 2, 3, 43, 44, 45, 46, 23, 24] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 557 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450665 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450665 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450665/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450665 Building REAL300024450666 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450666' /scratch/stefan/7786230/working/building/REAL300024450666 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450666 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450666/0 /scratch/stefan/7786230/working/building/REAL300024450666 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/546 `/scratch/stefan/7786230/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450666/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450666 none CC1C(NC(=O)C2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 19, 19, 19, 19, 19, 29, 29, 68, 109, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 68, 68, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 477 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: REAL300024450666 none CC1C(NC(=O)C2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [100, 100, 100, 100, 108, 108, 108, 201, 201, 201, 100, 100, 100, 98, 47, 98, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 108, 201, 201, 201, 201, 201, 100, 100, 100, 100, 100, 100, 47, 47, 1] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 626 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450666 none CC1C(NC(=O)C2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 11, 30, 100, 100, 100, 100, 100, 2, 2, 2, 1, 1, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 11, 11, 100] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450666 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450666 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450666/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450666 Building REAL300024450667 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450667' /scratch/stefan/7786230/working/building/REAL300024450667 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450667 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450667/0 /scratch/stefan/7786230/working/building/REAL300024450667 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/547 `/scratch/stefan/7786230/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450667/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450667 none CC1C(NC(=O)C2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 66, 120, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 66, 66, 201] 603 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 483 number of broken/clashed sets: 54 ./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: REAL300024450667 none CC1C(NC(=O)C2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 133, 133, 133, 201, 201, 201, 201, 201, 117, 117, 117, 115, 46, 115, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 133, 603, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 46, 46, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1246 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450667 none CC1C(NC(=O)C2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 13, 35, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 3, 33, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 117] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450667 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450667 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450667/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450667 Building REAL300024450668 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450668' /scratch/stefan/7786230/working/building/REAL300024450668 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450668 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450668/0 /scratch/stefan/7786230/working/building/REAL300024450668 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/548 `/scratch/stefan/7786230/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450668/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450668 none C=CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 95, 95, 95, 71, 71, 71, 71, 71, 69, 56, 69, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 95, 71, 71, 71, 71, 71, 71, 71, 56, 56, 1, 71, 71, 71, 71] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42]) total number of confs: 806 number of broken/clashed sets: 55 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450668 none C=CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 71, 71, 71, 71, 71, 1, 1, 47, 47, 47, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 71, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 279 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450668 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450668 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450668/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450668 Building REAL300024450669 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450669' /scratch/stefan/7786230/working/building/REAL300024450669 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450669 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450669/0 /scratch/stefan/7786230/working/building/REAL300024450669 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/549 `/scratch/stefan/7786230/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450669/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450669 none CC1C(NC(=O)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 39, 39, 63, 63, 63, 82, 82, 82, 82, 39, 39, 39, 39, 27, 39, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 63, 82, 82, 82, 82, 82, 82, 82, 82, 39, 39, 39, 39, 39, 39, 27, 27, 1] 82 rigid atoms, others: [47, 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, 43, 44, 45, 46]) total number of confs: 328 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450669 none CC1C(NC(=O)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 8, 13, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 8, 8, 39] 82 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 11, 12, 13, 14, 44, 43, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450669 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450669/1 /scratch/stefan/7786230/working/building/REAL300024450669 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/550 `/scratch/stefan/7786230/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450669.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450669/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450669 none CC1C(NC(=O)CN(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1] 4 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 13 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450669 none CC1C(NC(=O)CN(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2] 4 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 10, 11, 12, 13, 14, 43, 27, 28, 42] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450669 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450669 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450669/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450669/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450669 Building REAL300024450670 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450670' /scratch/stefan/7786230/working/building/REAL300024450670 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450670 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450670/0 /scratch/stefan/7786230/working/building/REAL300024450670 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/551 `/scratch/stefan/7786230/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N+]2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450670/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450670 none CC1C(NC(=O)C[N+]2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 8, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 30, 30, 8, 30, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 70, 70, 104, 138, 201, 201, 201, 201, 201, 47, 47, 47, 47, 47, 30, 8, 8, 1, 2, 2, 2, 1, 1, 47, 47, 47, 47, 47, 47, 104, 104, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 40, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 573 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: REAL300024450670 none CC1C(NC(=O)C[N+]2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 8, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 112, 112, 112, 186, 201, 201, 201, 201, 201, 79, 79, 79, 72, 29, 72, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 112, 186, 186, 201, 201, 201, 201, 201, 201, 79, 79, 79, 79, 79, 79, 29, 29, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 727 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450670 none CC1C(NC(=O)C[N+]2=CN(C)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 8, 1, 8, 5, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 23, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 3, 3, 12, 20, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 6, 23, 23, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 12, 12, 79] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450670 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450670 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450670/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450670 Building REAL300024450671 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450671' /scratch/stefan/7786230/working/building/REAL300024450671 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450671 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450671/0 /scratch/stefan/7786230/working/building/REAL300024450671 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/552 `/scratch/stefan/7786230/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450671/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450671 none CC1=NC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 86, 86, 86, 86, 86, 1, 1, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 86, 1, 2, 2, 2] 151 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 182 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: REAL300024450671 none CC1=NC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 151, 125, 125, 125, 86, 86, 86, 86, 86, 78, 39, 78, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 151, 151, 151, 151, 151, 125, 86, 86, 86, 86, 86, 86, 86, 39, 39, 1, 86, 86, 86, 86] 151 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 464 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450671 none CC1=NC=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 20, 20, 64, 92, 151, 151, 151, 151, 151, 12, 12, 2, 2, 2, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 64, 64, 151, 12, 12, 12, 12] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 414 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450671 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450671 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450671/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450671 Building REAL300024450672 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450672' /scratch/stefan/7786230/working/building/REAL300024450672 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450672 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450672/0 /scratch/stefan/7786230/working/building/REAL300024450672 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/553 `/scratch/stefan/7786230/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1C(C)C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450672/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450672 none CCOC1C(C)C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 38, 141, 141, 141, 141, 141, 1, 1, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 141, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 33 ./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: REAL300024450672 none CCOC1C(C)C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 199, 199, 199, 168, 168, 168, 141, 141, 141, 141, 141, 125, 32, 125, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 199, 199, 199, 199, 199, 199, 168, 141, 141, 141, 141, 141, 141, 141, 32, 32, 1, 141, 141, 141, 141] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 609 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450672 none CCOC1C(C)C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 12, 12, 43, 85, 199, 199, 199, 199, 199, 6, 6, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 4, 6, 6, 6, 6, 6, 6, 6, 43, 43, 199, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 434 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450672 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450672 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450672/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450672 Building REAL300024450673 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450673' /scratch/stefan/7786230/working/building/REAL300024450673 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450673 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450673/0 /scratch/stefan/7786230/working/building/REAL300024450673 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/554 `/scratch/stefan/7786230/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450673/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450673 none CC1C(NC(=O)C2CCC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 23, 29, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 23, 23, 34] 34 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 45, 36, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 120 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: REAL300024450673 none CC1C(NC(=O)C2CCC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 14, 20, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 14, 14, 1] 34 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 96 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450673 none CC1C(NC(=O)C2CCC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 8, 11, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 20] 34 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450673 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450673/1 /scratch/stefan/7786230/working/building/REAL300024450673 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/555 `/scratch/stefan/7786230/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450673.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450673/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450673 none CC1C(NC(=O)C2CCC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 13, 44, 11, 40, 45, 36, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 23 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: REAL300024450673 none CC1C(NC(=O)C2CCC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 6 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450673 none CC1C(NC(=O)C2CCC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 4, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 6] 6 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450673 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450673 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450673/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450673/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450673 Building REAL300024450674 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450674' /scratch/stefan/7786230/working/building/REAL300024450674 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450674 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450674/0 /scratch/stefan/7786230/working/building/REAL300024450674 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/556 `/scratch/stefan/7786230/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450674/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450674 none C=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 12 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 17 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450674 none C=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 2, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 9, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 12 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 34 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450674 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450674 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450674/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450674 Building REAL300024450675 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450675' /scratch/stefan/7786230/working/building/REAL300024450675 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450675 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450675/0 /scratch/stefan/7786230/working/building/REAL300024450675 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/557 `/scratch/stefan/7786230/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450675/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450675 none CC1C(NC(=O)CCCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 40, 40, 41, 41, 41, 136, 122, 181, 201, 201, 40, 40, 40, 40, 26, 40, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 41, 136, 136, 155, 155, 165, 165, 40, 40, 40, 40, 40, 40, 26, 26, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 951 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450675 none CC1C(NC(=O)CCCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 17, 43, 75, 75, 1, 1, 1, 1, 1, 3, 3, 7, 12, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 3, 12, 12, 22, 22, 38, 41, 1, 1, 1, 1, 1, 1, 7, 7, 40] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450675 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450675 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450675/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450675 Building REAL300024450676 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450676' /scratch/stefan/7786230/working/building/REAL300024450676 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450676 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450676/0 /scratch/stefan/7786230/working/building/REAL300024450676 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/558 `/scratch/stefan/7786230/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(F)(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450676/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450676 none CC(O)C(F)(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 185, 201, 114, 185, 185, 114, 114, 72, 72, 72, 72, 72, 70, 49, 70, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 201, 201, 603, 114, 72, 72, 72, 72, 72, 72, 72, 49, 49, 1, 72, 72, 72, 72] 603 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 1433 number of broken/clashed sets: 207 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450676 none CC(O)C(F)(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 22, 37, 6, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 72, 72, 72, 72, 72, 1, 1, 37, 37, 37, 37, 111, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 72, 1, 2, 2, 2] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 408 number of broken/clashed sets: 207 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450676 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450676 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450676/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450676 Building REAL300024450677 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450677' /scratch/stefan/7786230/working/building/REAL300024450677 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450677 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450677/0 /scratch/stefan/7786230/working/building/REAL300024450677 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/559 `/scratch/stefan/7786230/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2OCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450677/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450677 none CC1C(NC(=O)C2OCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 42, 99, 187, 187, 187, 187, 187, 6, 6, 6, 6, 6, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 42, 42, 187] 187 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 399 number of broken/clashed sets: 29 ./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: REAL300024450677 none CC1C(NC(=O)C2OCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [180, 180, 180, 180, 186, 186, 186, 187, 187, 187, 187, 187, 180, 180, 180, 168, 65, 168, 13, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 186, 187, 187, 187, 187, 187, 187, 187, 187, 187, 180, 180, 180, 180, 180, 180, 65, 65, 1] 187 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 542 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450677 none CC1C(NC(=O)C2OCC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 18, 64, 180, 180, 180, 180, 180, 2, 2, 2, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 18, 18, 180] 187 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 305 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450677 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450677 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450677/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450677 Building REAL300024450678 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450678' /scratch/stefan/7786230/working/building/REAL300024450678 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450678 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450678/0 /scratch/stefan/7786230/working/building/REAL300024450678 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/560 `/scratch/stefan/7786230/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450678/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450678 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 48, 48, 88, 129, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 29, 5, 5, 1, 2, 2, 2, 36, 36, 36, 36, 36, 36, 88, 88, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47]) total number of confs: 548 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: REAL300024450678 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 100, 100, 100, 190, 201, 201, 201, 201, 201, 76, 76, 76, 71, 27, 71, 11, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 100, 190, 190, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 27, 27, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450678 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 20, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 10, 17, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 3, 20, 20, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 10, 10, 76] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450678 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450678 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450678/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450678 Building REAL300024450679 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450679' /scratch/stefan/7786230/working/building/REAL300024450679 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450679 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450679/0 /scratch/stefan/7786230/working/building/REAL300024450679 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/561 `/scratch/stefan/7786230/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450679/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450679 none CC1=NN(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 32, 86, 86, 86, 86, 86, 1, 1, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 86, 1, 2, 2, 2] 158 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 31 ./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: REAL300024450679 none CC1=NN(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 136, 136, 136, 86, 86, 86, 86, 86, 80, 39, 80, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 158, 158, 158, 158, 158, 158, 158, 136, 86, 86, 86, 86, 86, 86, 86, 39, 39, 1, 86, 86, 86, 86] 158 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 486 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450679 none CC1=NN(C)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 21, 21, 66, 99, 158, 158, 158, 158, 158, 14, 14, 1, 2, 2, 2, 2, 2, 2, 5, 14, 14, 14, 14, 14, 14, 14, 66, 66, 158, 14, 14, 14, 14] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 424 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450679 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450679 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450679/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450679 Building REAL300024450680 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450680' /scratch/stefan/7786230/working/building/REAL300024450680 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450680 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450680/0 /scratch/stefan/7786230/working/building/REAL300024450680 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/562 `/scratch/stefan/7786230/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CCC1) `REAL300024450680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450680/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 151, 151, 151, 125, 125, 125, 125, 125, 109, 29, 109, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 151, 125, 125, 125, 125, 125, 125, 125, 29, 29, 1, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 690 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: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 12, 12, 12, 16, 16, 16, 16, 16, 26, 26, 81, 130, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 3, 3, 3, 3, 12, 16, 16, 16, 16, 16, 16, 16, 81, 81, 201, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 31, 125, 125, 125, 125, 125, 1, 1, 12, 16, 16, 16, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 125, 1, 2, 2, 2, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 41, 36, 37, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 246 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450680 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450680/1 /scratch/stefan/7786230/working/building/REAL300024450680 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/563 `/scratch/stefan/7786230/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CCC1) `REAL300024450680.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450680/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 25, 25, 25, 25, 22, 14, 22, 10, 1, 1, 1, 1, 1, 1, 1, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 25, 25, 25, 25, 25, 14, 14, 1, 25, 25, 25, 25, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 72 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: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 6, 6, 6, 8, 8, 8, 8, 8, 9, 9, 17, 22, 27, 27, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 8, 8, 8, 8, 8, 8, 8, 17, 17, 27, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 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]) total number of confs: 85 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450680 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 25, 25, 25, 25, 25, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8] 27 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 87 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450680 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450680 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450680/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450680/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450680 Building REAL300024450681 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450681' /scratch/stefan/7786230/working/building/REAL300024450681 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450681 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450681/0 /scratch/stefan/7786230/working/building/REAL300024450681 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/564 `/scratch/stefan/7786230/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450681/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450681 none CC1C(NC(=O)[C@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 27, 27, 64, 111, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 17, 17, 17, 17, 17, 17, 64, 64, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 485 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: REAL300024450681 none CC1C(NC(=O)[C@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 94, 94, 94, 201, 201, 201, 201, 201, 71, 71, 71, 71, 38, 71, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 94, 201, 201, 71, 71, 71, 71, 71, 71, 38, 38, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 627 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450681 none CC1C(NC(=O)[C@H]2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 11, 23, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 17, 17, 1, 1, 1, 1, 1, 1, 11, 11, 71] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450681 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450681 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450681/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450681 Building REAL300024450682 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450682' /scratch/stefan/7786230/working/building/REAL300024450682 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450682 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450682/0 /scratch/stefan/7786230/working/building/REAL300024450682 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/565 `/scratch/stefan/7786230/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450682/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450682 none CC1C(NC(=O)CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 43, 43, 86, 127, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 15, 6, 6, 1, 1, 1, 36, 36, 36, 36, 36, 36, 86, 86, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 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: REAL300024450682 none CC1C(NC(=O)CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 61, 61, 61, 90, 90, 90, 193, 201, 201, 201, 201, 61, 61, 61, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 90, 193, 193, 201, 201, 201, 61, 61, 61, 61, 61, 61, 36, 36, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 802 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450682 none CC1C(NC(=O)CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 17, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 9, 16, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 5, 17, 17, 27, 27, 27, 1, 1, 1, 1, 1, 1, 9, 9, 61] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 184 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450682 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450682 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450682/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450682 Building REAL300024450683 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450683' /scratch/stefan/7786230/working/building/REAL300024450683 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450683 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450683/0 /scratch/stefan/7786230/working/building/REAL300024450683 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/566 `/scratch/stefan/7786230/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450683/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450683 none CC1C(NC(=O)C(C)(C)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [102, 102, 102, 102, 160, 160, 160, 196, 196, 196, 201, 201, 201, 201, 102, 102, 102, 100, 34, 100, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 160, 196, 196, 196, 196, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 102, 34, 34, 1] 201 rigid atoms, others: [56, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 745 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450683 none CC1C(NC(=O)C(C)(C)C[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 10, 10, 10, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 22, 102, 102, 102, 102, 102, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 102] 201 rigid atoms, others: [0, 1, 2, 3, 49, 16, 32, 18, 14, 15, 48, 17, 50, 51, 52, 53, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450683 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450683 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450683/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450683 Building REAL300024450684 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450684' /scratch/stefan/7786230/working/building/REAL300024450684 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450684 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450684/0 /scratch/stefan/7786230/working/building/REAL300024450684 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/567 `/scratch/stefan/7786230/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450684/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450684 none CC(C)NC(=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 200, 171, 200, 171, 171, 105, 105, 105, 105, 105, 98, 32, 98, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 200, 171, 105, 105, 105, 105, 105, 105, 105, 32, 32, 1, 105, 105, 105, 105] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 625 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450684 none CC(C)NC(=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 20, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 30, 105, 105, 105, 105, 105, 1, 1, 20, 20, 20, 20, 20, 20, 20, 11, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 105, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450684 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450684 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450684/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450684 Building REAL300024450685 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450685' /scratch/stefan/7786230/working/building/REAL300024450685 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450685 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450685/0 /scratch/stefan/7786230/working/building/REAL300024450685 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/568 `/scratch/stefan/7786230/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Cl)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450685/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450685 none C=C(Cl)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 186, 201, 169, 54, 54, 54, 47, 47, 47, 47, 47, 46, 25, 46, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 201, 201, 186, 186, 169, 169, 54, 47, 47, 47, 47, 47, 47, 47, 25, 25, 1, 47, 47, 47, 47] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 769 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450685 none C=C(Cl)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 42, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 47, 47, 47, 47, 47, 1, 1, 42, 42, 23, 23, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450685 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450685 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450685/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450685 Building REAL300024450686 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450686' /scratch/stefan/7786230/working/building/REAL300024450686 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450686 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450686/0 /scratch/stefan/7786230/working/building/REAL300024450686 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/569 `/scratch/stefan/7786230/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CCOC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450686/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450686 none CCC(CCOC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [130, 135, 83, 135, 150, 201, 201, 83, 83, 74, 74, 74, 74, 74, 69, 28, 69, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 136, 136, 136, 136, 136, 135, 150, 150, 201, 201, 201, 201, 201, 83, 74, 74, 74, 74, 74, 74, 74, 28, 28, 1, 74, 74, 74, 74] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 967 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450686 none CCC(CCOC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 3, 9, 14, 22, 34, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 74, 74, 74, 74, 74, 1, 1, 11, 11, 11, 11, 11, 9, 14, 14, 22, 22, 34, 34, 34, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 74, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 271 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450686 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450686 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450686/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450686 Building REAL300024450687 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450687' /scratch/stefan/7786230/working/building/REAL300024450687 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450687 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450687/0 /scratch/stefan/7786230/working/building/REAL300024450687 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/570 `/scratch/stefan/7786230/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1) `REAL300024450687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450687/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450687 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 30, 91, 91, 91, 91, 91, 1, 1, 14, 14, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 91, 1, 2, 2, 2, 14, 14, 14, 14] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 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: REAL300024450687 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 100, 100, 100, 91, 91, 91, 91, 91, 90, 45, 90, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 100, 91, 91, 91, 91, 91, 91, 91, 45, 45, 1, 91, 91, 91, 91, 201, 201, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 471 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450687 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 14, 14, 14, 14, 14, 23, 23, 68, 113, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 14, 68, 68, 201, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 502 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450687 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450687 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450687/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450687 Building REAL300024450688 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450688' /scratch/stefan/7786230/working/building/REAL300024450688 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450688 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450688/0 /scratch/stefan/7786230/working/building/REAL300024450688 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/571 `/scratch/stefan/7786230/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450688/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450688 none CC1C(NC(=O)C2=COC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 12, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 61, 115, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13, 13, 13, 13, 13, 13, 61, 61, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 470 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: REAL300024450688 none CC1C(NC(=O)C2=COC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 12, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 116, 116, 116, 201, 201, 201, 201, 201, 201, 79, 79, 79, 77, 42, 77, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 116, 201, 201, 201, 79, 79, 79, 79, 79, 79, 42, 42, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 555 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450688 none CC1C(NC(=O)C2=COC(=O)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 12, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 27, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 5, 13, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 79] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450688 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450688 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450688/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450688 Building REAL300024450689 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450689' /scratch/stefan/7786230/working/building/REAL300024450689 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450689 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450689/0 /scratch/stefan/7786230/working/building/REAL300024450689 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/572 `/scratch/stefan/7786230/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450689/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450689 none CC1C(NC(=O)C=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 74, 113, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 74, 74, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 513 number of broken/clashed sets: 39 ./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: REAL300024450689 none CC1C(NC(=O)C=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 76, 76, 76, 201, 201, 201, 201, 201, 69, 69, 69, 66, 36, 66, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 36, 36, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 598 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450689 none CC1C(NC(=O)C=C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 14, 23, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 14, 14, 69] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450689 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450689 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450689/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450689 Building REAL300024450690 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450690' /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450690 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450690/0 /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/573 `/scratch/stefan/7786230/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450690/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)C[N@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 3, 5, 2, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 14, 18, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 14, 14, 22] 22 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 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: REAL300024450690 none CC1C(NC(=O)C[N@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 21, 21, 21, 22, 22, 22, 22, 22, 22, 19, 19, 19, 19, 15, 19, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 19, 19, 19, 19, 19, 19, 15, 15, 1] 22 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 68 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)C[N@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 4, 7, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 19] 22 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450690/1 /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/574 `/scratch/stefan/7786230/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450690.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450690/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)C[N@@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 6, 6, 3, 6, 2, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 14, 15, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 6, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 14, 14, 19] 19 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 7, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 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: REAL300024450690 none CC1C(NC(=O)C[N@@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 18, 18, 18, 18, 19, 19, 19, 19, 19, 15, 15, 15, 15, 13, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 13, 13, 1] 19 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 52 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)C[N@@H+](C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 4, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 3, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 15] 19 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 61 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450690/2 /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/575 `/scratch/stefan/7786230/working/3D/575' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450690.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450690/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)CN(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 17, 17, 7, 17, 3, 1, 3, 1, 1, 1, 30, 30, 30, 30, 30, 42, 42, 78, 121, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 17, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 78, 78, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 511 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: REAL300024450690 none CC1C(NC(=O)CN(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [117, 117, 117, 117, 162, 162, 162, 200, 201, 201, 201, 201, 117, 117, 117, 110, 29, 110, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 162, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 29, 29, 1] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 679 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450690 none CC1C(NC(=O)CN(C)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 29, 29, 30, 30, 1, 1, 1, 1, 1, 3, 3, 12, 29, 117, 117, 117, 117, 117, 2, 2, 2, 1, 1, 6, 19, 19, 29, 29, 29, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 12, 12, 117] 201 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 288 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450690 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450690 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450690/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450690/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450690/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450690 Building REAL300024450691 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450691' /scratch/stefan/7786230/working/building/REAL300024450691 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450691 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450691/0 /scratch/stefan/7786230/working/building/REAL300024450691 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/576 `/scratch/stefan/7786230/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CO)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450691/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450691 none CC1C(NC(=O)C2(CO)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 3, 1, 3, 1, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 9 rigid atoms, others: [35, 4, 37, 6, 7, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 8, 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]) total number of confs: 25 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: REAL300024450691 none CC1C(NC(=O)C2(CO)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 9, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 9 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 16 number of broken/clashed sets: 4 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450691 none CC1C(NC(=O)C2(CO)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 9 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 26 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450691 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450691 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450691/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450691 Building REAL300024450692 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450692' /scratch/stefan/7786230/working/building/REAL300024450692 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450692 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450692/0 /scratch/stefan/7786230/working/building/REAL300024450692 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/577 `/scratch/stefan/7786230/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450692/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450692 none CC(C)=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 193, 183, 68, 68, 68, 54, 54, 54, 54, 54, 52, 23, 52, 12, 1, 1, 1, 1, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 193, 193, 183, 183, 68, 54, 54, 54, 54, 54, 54, 54, 23, 23, 1, 54, 54, 54, 54] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 778 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450692 none CC(C)=CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 26, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 54, 54, 54, 54, 54, 1, 1, 32, 32, 32, 32, 32, 32, 32, 26, 26, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450692 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450692 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450692/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450692 Building REAL300024450693 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450693' /scratch/stefan/7786230/working/building/REAL300024450693 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450693 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450693/0 /scratch/stefan/7786230/working/building/REAL300024450693 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/578 `/scratch/stefan/7786230/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC) `REAL300024450693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450693/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450693 none CC=C(C=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [147, 147, 85, 85, 45, 45, 45, 42, 42, 42, 42, 42, 42, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 147, 201, 147, 147, 147, 147, 85, 85, 45, 42, 42, 42, 42, 42, 42, 42, 26, 26, 1, 42, 42, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 813 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450693 none CC=C(C=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 12, 42, 42, 42, 42, 42, 1, 1, 27, 44, 27, 27, 27, 27, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 1, 2, 2, 2, 44, 44, 44, 44, 44] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 261 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450693 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450693 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450693/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450693 Building REAL300024450694 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450694' /scratch/stefan/7786230/working/building/REAL300024450694 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450694 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450694/0 /scratch/stefan/7786230/working/building/REAL300024450694 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/579 `/scratch/stefan/7786230/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450694/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450694 none CC1C(NC(=O)C2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 66, 120, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 66, 66, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 465 number of broken/clashed sets: 28 ./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: REAL300024450694 none CC1C(NC(=O)C2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 104, 104, 105, 105, 105, 201, 201, 201, 104, 104, 104, 103, 54, 103, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 105, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 104, 54, 54, 1] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 629 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450694 none CC1C(NC(=O)C2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 13, 34, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 104] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450694 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450694 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450694/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450694 Building REAL300024450695 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450695' /scratch/stefan/7786230/working/building/REAL300024450695 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450695 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450695/0 /scratch/stefan/7786230/working/building/REAL300024450695 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/580 `/scratch/stefan/7786230/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450695/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450695 none CC1C(NC(=O)C=CC2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 29, 29, 7, 29, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 45, 45, 90, 123, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 90, 90, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 518 number of broken/clashed sets: 34 ./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: REAL300024450695 none CC1C(NC(=O)C=CC2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 68, 68, 68, 180, 180, 201, 201, 201, 201, 66, 66, 66, 65, 38, 65, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 68, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 38, 38, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 621 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450695 none CC1C(NC(=O)C=CC2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 14, 14, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 13, 22, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 4, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 13, 13, 66] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 212 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450695 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450695 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450695/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450695 Building REAL300024450696 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450696' /scratch/stefan/7786230/working/building/REAL300024450696 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450696 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450696/0 /scratch/stefan/7786230/working/building/REAL300024450696 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/581 `/scratch/stefan/7786230/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450696/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450696 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 33, 86, 86, 86, 86, 86, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 86, 1, 2, 2, 2] 139 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 29 ./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: REAL300024450696 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [139, 139, 139, 139, 112, 112, 112, 86, 86, 86, 86, 86, 75, 40, 75, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 112, 86, 86, 86, 86, 86, 86, 86, 40, 40, 1, 86, 86, 86, 86] 139 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 449 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450696 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 16, 25, 25, 58, 85, 139, 139, 139, 139, 139, 16, 16, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 58, 58, 139, 16, 16, 16, 16] 139 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 376 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450696 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450696 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450696/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450696 Building REAL300024450697 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450697' /scratch/stefan/7786230/working/building/REAL300024450697 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450697 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450697/0 /scratch/stefan/7786230/working/building/REAL300024450697 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/582 `/scratch/stefan/7786230/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450697/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450697 none CC1C(NC(=O)C2CCCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 22, 22, 79, 115, 178, 178, 178, 178, 178, 15, 15, 15, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 79, 79, 178] 178 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 460 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: REAL300024450697 none CC1C(NC(=O)C2CCCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 114, 114, 114, 178, 178, 178, 178, 178, 107, 107, 107, 100, 43, 100, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 114, 178, 178, 178, 178, 178, 178, 178, 178, 178, 107, 107, 107, 107, 107, 107, 43, 43, 1] 178 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 558 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450697 none CC1C(NC(=O)C2CCCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 15, 33, 107, 107, 107, 107, 107, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 15, 15, 107] 178 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450697 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450697 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450697/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450697 Building REAL300024450698 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450698' /scratch/stefan/7786230/working/building/REAL300024450698 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450698 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450698/0 /scratch/stefan/7786230/working/building/REAL300024450698 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/583 `/scratch/stefan/7786230/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450698/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450698 none CC1=NOC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 5, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 118, 118, 118, 118, 118, 1, 1, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 118, 1, 2, 2, 2, 16, 16] 157 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 29 ./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: REAL300024450698 none CC1=NOC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 132, 157, 132, 132, 118, 118, 118, 118, 118, 109, 44, 109, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 157, 157, 157, 157, 157, 157, 157, 132, 118, 118, 118, 118, 118, 118, 118, 44, 44, 1, 118, 118, 118, 118, 157, 157] 157 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 495 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450698 none CC1=NOC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 16, 21, 21, 67, 99, 157, 157, 157, 157, 157, 16, 16, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 67, 67, 157, 16, 16, 16, 16, 1, 1] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 49, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 397 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450698 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450698 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450698/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450698 Building REAL300024450699 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450699' /scratch/stefan/7786230/working/building/REAL300024450699 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450699 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450699/0 /scratch/stefan/7786230/working/building/REAL300024450699 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/584 `/scratch/stefan/7786230/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(CO)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450699/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450699 none CC1C(NC(=O)C2=NN(CO)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 9, 1, 1, 7, 7, 7, 7, 7, 13, 13, 37, 59, 125, 125, 125, 125, 125, 7, 7, 7, 7, 7, 3, 9, 9, 27, 1, 1, 7, 7, 7, 7, 7, 7, 37, 37, 125] 375 rigid atoms, others: [4, 37, 6, 7, 8, 9, 11, 12, 36] set([0, 1, 2, 3, 5, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 333 number of broken/clashed sets: 75 ./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: REAL300024450699 none CC1C(NC(=O)C2=NN(CO)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 116, 116, 116, 125, 125, 125, 125, 125, 125, 86, 86, 86, 81, 39, 81, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 116, 125, 125, 375, 125, 125, 86, 86, 86, 86, 86, 86, 39, 39, 1] 375 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 777 number of broken/clashed sets: 75 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450699 none CC1C(NC(=O)C2=NN(CO)C=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 5, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 22, 7, 7, 1, 1, 1, 1, 1, 3, 3, 15, 30, 86, 86, 86, 86, 86, 2, 2, 2, 1, 1, 5, 22, 22, 66, 7, 7, 1, 1, 1, 1, 1, 1, 15, 15, 86] 375 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 297 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450699 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450699 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450699/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450699 Building REAL300024450700 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450700' /scratch/stefan/7786230/working/building/REAL300024450700 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450700 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450700/0 /scratch/stefan/7786230/working/building/REAL300024450700 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/585 `/scratch/stefan/7786230/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450700/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450700 none CC1C(NC(=O)CC2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 18, 18, 5, 18, 1, 1, 1, 10, 1, 1, 20, 20, 20, 20, 20, 31, 31, 67, 109, 201, 201, 201, 201, 201, 20, 20, 20, 20, 20, 18, 5, 5, 10, 10, 30, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 67, 67, 201] 603 rigid atoms, others: [37, 6, 7, 8, 10, 11, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 555 number of broken/clashed sets: 113 ./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: REAL300024450700 none CC1C(NC(=O)CC2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 90, 90, 90, 179, 201, 201, 201, 201, 89, 89, 89, 84, 31, 84, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 90, 179, 179, 201, 201, 603, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 31, 31, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1342 number of broken/clashed sets: 113 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450700 none CC1C(NC(=O)CC2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 20, 34, 20, 20, 1, 1, 1, 1, 1, 3, 3, 11, 23, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 3, 12, 12, 34, 34, 102, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 11, 11, 89] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 390 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450700 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450700 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450700/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450700 Building REAL300024450701 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450701' /scratch/stefan/7786230/working/building/REAL300024450701 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450701 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450701/0 /scratch/stefan/7786230/working/building/REAL300024450701 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/586 `/scratch/stefan/7786230/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2C[NH+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450701/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450701 none CC1C(NC(=O)CC2C[NH+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 25, 25, 5, 25, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 63, 82, 106, 106, 106, 106, 106, 32, 32, 32, 32, 32, 25, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 63, 63, 106] 106 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 327 number of broken/clashed sets: 39 ./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: REAL300024450701 none CC1C(NC(=O)CC2C[NH+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 89, 89, 89, 104, 106, 106, 106, 106, 106, 74, 74, 74, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 89, 104, 104, 106, 106, 106, 106, 106, 106, 106, 106, 74, 74, 74, 74, 74, 74, 29, 29, 1] 106 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 377 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450701 none CC1C(NC(=O)CC2C[NH+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 16, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 8, 17, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 4, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 8, 8, 74] 106 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450701 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450701 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450701/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450701 Building REAL300024450702 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450702' /scratch/stefan/7786230/working/building/REAL300024450702 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450702 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450702/0 /scratch/stefan/7786230/working/building/REAL300024450702 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/587 `/scratch/stefan/7786230/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1) `REAL300024450702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450702/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450702 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 24, 60, 60, 60, 60, 60, 1, 1, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 60, 1, 2, 2, 2] 77 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 136 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: REAL300024450702 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 77, 77, 77, 61, 61, 61, 60, 60, 60, 60, 60, 59, 36, 59, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 77, 77, 77, 77, 61, 60, 60, 60, 60, 60, 60, 60, 36, 36, 1, 60, 60, 60, 60] 77 rigid atoms, others: [39, 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, 37, 38, 40, 41, 42, 43]) total number of confs: 237 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450702 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 10, 10, 32, 47, 77, 77, 77, 77, 77, 8, 8, 1, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 8, 32, 32, 77, 8, 8, 8, 8] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25] set([6, 7, 8, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450702 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450702 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450702/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450702 Building REAL300024450703 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450703' /scratch/stefan/7786230/working/building/REAL300024450703 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450703 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450703/0 /scratch/stefan/7786230/working/building/REAL300024450703 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/588 `/scratch/stefan/7786230/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(C)(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450703/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450703 none CC1C(NC(=O)C2CC(C)(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 25, 25, 75, 117, 201, 201, 201, 201, 201, 18, 18, 18, 18, 18, 12, 1, 1, 1, 2, 2, 2, 6, 1, 1, 18, 18, 18, 18, 18, 18, 75, 75, 201] 603 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 40, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 508 number of broken/clashed sets: 136 ./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: REAL300024450703 none CC1C(NC(=O)C2CC(C)(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 87, 87, 87, 91, 91, 91, 201, 201, 201, 201, 201, 87, 87, 87, 80, 43, 80, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 91, 201, 201, 201, 201, 201, 201, 603, 201, 201, 87, 87, 87, 87, 87, 87, 43, 43, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1223 number of broken/clashed sets: 136 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450703 none CC1C(NC(=O)C2CC(C)(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 14, 28, 87, 87, 87, 87, 87, 2, 2, 2, 1, 1, 4, 18, 18, 18, 18, 18, 18, 54, 18, 18, 1, 1, 1, 1, 1, 1, 14, 14, 87] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450703 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450703 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450703/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450703 Building REAL300024450704 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450704' /scratch/stefan/7786230/working/building/REAL300024450704 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450704 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450704/0 /scratch/stefan/7786230/working/building/REAL300024450704 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/589 `/scratch/stefan/7786230/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450704/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450704 none CCCCCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 192, 199, 189, 134, 62, 134, 62, 62, 51, 51, 51, 51, 51, 50, 24, 50, 11, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 199, 199, 198, 198, 134, 402, 62, 51, 51, 51, 51, 51, 51, 51, 24, 24, 1, 51, 51, 51, 51] 603 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 1408 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450704 none CCCCCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 34, 33, 31, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 51, 51, 51, 51, 51, 1, 1, 35, 35, 35, 35, 35, 35, 35, 33, 33, 32, 32, 13, 39, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 51, 1, 2, 2, 2] 603 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 295 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450704 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450704 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450704/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450704 Building REAL300024450705 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450705' /scratch/stefan/7786230/working/building/REAL300024450705 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450705 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450705/0 /scratch/stefan/7786230/working/building/REAL300024450705 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/590 `/scratch/stefan/7786230/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450705/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450705 none CO[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 176, 150, 178, 178, 150, 150, 79, 79, 79, 79, 79, 78, 55, 78, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 178, 178, 178, 178, 178, 178, 150, 79, 79, 79, 79, 79, 79, 79, 55, 55, 1, 79, 79, 79, 79] 178 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 653 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450705 none CO[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [31, 26, 6, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 79, 79, 79, 79, 79, 1, 1, 31, 31, 31, 28, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 79, 1, 2, 2, 2] 178 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 237 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450705 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450705 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450705/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450705 Building REAL300024450706 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450706' /scratch/stefan/7786230/working/building/REAL300024450706 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450706 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450706/0 /scratch/stefan/7786230/working/building/REAL300024450706 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/591 `/scratch/stefan/7786230/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCN2C=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450706/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450706 none CC1C(NC(=O)C2CCCN2C=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 6, 6, 6] 6 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 21 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: REAL300024450706 none CC1C(NC(=O)C2CCCN2C=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 1] 6 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 10 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450706 none CC1C(NC(=O)C2CCCN2C=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 5] 6 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 33 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450706 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450706 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450706/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450706 Building REAL300024450707 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450707' /scratch/stefan/7786230/working/building/REAL300024450707 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450707 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450707/0 /scratch/stefan/7786230/working/building/REAL300024450707 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/592 `/scratch/stefan/7786230/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450707/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450707 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 29, 67, 67, 67, 67, 67, 1, 1, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 67, 1, 2, 2, 2] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 147 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: REAL300024450707 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 67, 67, 67, 67, 67, 66, 40, 66, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 68, 68, 68, 68, 68, 68, 67, 67, 67, 67, 67, 67, 67, 40, 40, 1, 67, 67, 67, 67] 68 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450707 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 6, 6, 22, 36, 68, 68, 68, 68, 68, 5, 5, 1, 2, 2, 2, 1, 3, 5, 5, 5, 5, 5, 5, 5, 22, 22, 68, 5, 5, 5, 5] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450707 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450707/1 /scratch/stefan/7786230/working/building/REAL300024450707 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/593 `/scratch/stefan/7786230/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450707.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450707/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450707 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 34, 97, 97, 97, 97, 97, 1, 1, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 97, 1, 2, 2, 2, 8] 116 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 22 ./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: REAL300024450707 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 97, 97, 97, 97, 97, 91, 41, 91, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 116, 116, 116, 116, 116, 97, 97, 97, 97, 97, 97, 97, 41, 41, 1, 97, 97, 97, 97, 116] 116 rigid atoms, others: [39, 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, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 372 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450707 none CC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 13, 13, 47, 67, 116, 116, 116, 116, 116, 8, 8, 1, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 47, 47, 116, 8, 8, 8, 8, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 25] set([6, 7, 8, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 304 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450707 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450707 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450707/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450707/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450707 Building REAL300024450708 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450708' /scratch/stefan/7786230/working/building/REAL300024450708 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450708 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450708/0 /scratch/stefan/7786230/working/building/REAL300024450708 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/594 `/scratch/stefan/7786230/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450708/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450708 none CC1=CN=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 64, 64, 64, 64, 64, 1, 1, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 64, 1, 2, 2, 2, 9] 84 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 146 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: REAL300024450708 none CC1=CN=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 80, 80, 80, 64, 64, 64, 64, 64, 61, 37, 61, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 84, 84, 84, 84, 84, 80, 64, 64, 64, 64, 64, 64, 64, 37, 37, 1, 64, 64, 64, 64, 84] 84 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 274 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450708 none CC1=CN=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 12, 12, 37, 51, 84, 84, 84, 84, 84, 9, 9, 1, 2, 2, 2, 1, 5, 9, 9, 9, 9, 9, 9, 9, 37, 37, 84, 9, 9, 9, 9, 1] 84 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450708 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450708 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450708/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450708 Building REAL300024450709 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450709' /scratch/stefan/7786230/working/building/REAL300024450709 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450709 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450709/0 /scratch/stefan/7786230/working/building/REAL300024450709 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/595 `/scratch/stefan/7786230/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450709/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450709 none CC1C(NC(=O)[C@@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 38, 38, 85, 132, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 8, 1, 1, 7, 25, 25, 25, 25, 25, 25, 85, 85, 201] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 577 number of broken/clashed sets: 94 ./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: REAL300024450709 none CC1C(NC(=O)[C@@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [63, 63, 63, 63, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 63, 63, 63, 60, 47, 60, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 131, 201, 201, 201, 63, 63, 63, 63, 63, 63, 47, 47, 1] 201 rigid atoms, others: [45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 652 number of broken/clashed sets: 94 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450709 none CC1C(NC(=O)[C@@H]2C[C@@H]2C(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 25, 25, 25, 25, 25, 50, 50, 1, 1, 1, 1, 1, 3, 3, 8, 16, 63, 63, 63, 63, 63, 2, 2, 2, 1, 1, 6, 25, 25, 50, 1, 1, 1, 1, 1, 1, 8, 8, 63] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 32, 40, 41, 42, 39, 14, 15, 16, 17, 18, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 299 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450709 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450709 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450709/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450709 Building REAL300024450710 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450710' /scratch/stefan/7786230/working/building/REAL300024450710 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450710 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450710/0 /scratch/stefan/7786230/working/building/REAL300024450710 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/596 `/scratch/stefan/7786230/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450710/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 24, 24, 57, 97, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 7, 1, 1, 17, 17, 17, 17, 17, 17, 57, 57, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 452 number of broken/clashed sets: 18 ./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: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [123, 123, 123, 123, 129, 129, 129, 201, 201, 201, 201, 201, 123, 123, 123, 120, 58, 120, 13, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 129, 201, 201, 123, 123, 123, 123, 123, 123, 58, 58, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 551 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 11, 33, 123, 123, 123, 123, 123, 2, 2, 2, 1, 1, 5, 17, 17, 1, 1, 1, 1, 1, 1, 11, 11, 123] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 213 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450710 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450710/1 /scratch/stefan/7786230/working/building/REAL300024450710 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/597 `/scratch/stefan/7786230/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450710.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450710/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 48, 108, 192, 192, 192, 192, 192, 8, 8, 8, 8, 8, 4, 1, 8, 8, 8, 8, 8, 8, 48, 48, 192] 192 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 408 number of broken/clashed sets: 24 ./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: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 192, 192, 192, 192, 192, 192, 192, 192, 164, 164, 164, 159, 52, 159, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 192, 192, 164, 164, 164, 164, 164, 164, 52, 52, 1] 192 rigid atoms, others: [41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 577 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450710 none CC1C(NC(=O)C2=COC(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 16, 51, 164, 164, 164, 164, 164, 2, 2, 2, 1, 1, 6, 8, 1, 1, 1, 1, 1, 1, 16, 16, 164] 192 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450710 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450710 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450710/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450710/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450710 Building REAL300024450711 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450711' /scratch/stefan/7786230/working/building/REAL300024450711 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450711 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450711/0 /scratch/stefan/7786230/working/building/REAL300024450711 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/598 `/scratch/stefan/7786230/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450711/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450711 none CC=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 185, 110, 185, 110, 110, 91, 91, 91, 91, 91, 83, 31, 83, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 185, 555, 110, 91, 91, 91, 91, 91, 91, 91, 31, 31, 1, 91, 91, 91, 91] 603 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 1321 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450711 none CC=CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 91, 91, 91, 91, 91, 1, 1, 44, 44, 44, 44, 44, 17, 51, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 91, 1, 2, 2, 2] 603 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 332 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450711 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450711 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450711/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450711 Building REAL300024450712 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450712' /scratch/stefan/7786230/working/building/REAL300024450712 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450712 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450712/0 /scratch/stefan/7786230/working/building/REAL300024450712 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/599 `/scratch/stefan/7786230/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450712/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450712 none CCCC[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 167, 77, 167, 167, 77, 77, 53, 53, 53, 53, 53, 51, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 77, 53, 53, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53, 53, 53] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 837 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450712 none CCCC[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 25, 24, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 53, 53, 53, 53, 53, 1, 1, 28, 28, 28, 28, 28, 25, 25, 25, 25, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 53, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450712 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450712 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450712/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450712 Building REAL300024450713 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450713' /scratch/stefan/7786230/working/building/REAL300024450713 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450713 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450713/0 /scratch/stefan/7786230/working/building/REAL300024450713 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/600 `/scratch/stefan/7786230/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450713/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450713 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 82, 117, 82, 82, 40, 40, 40, 40, 40, 40, 29, 40, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 117, 117, 117, 117, 117, 117, 117, 82, 40, 40, 40, 40, 40, 40, 40, 29, 29, 1, 40, 40, 40, 40, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 434 number of broken/clashed sets: 109 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450713 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 40, 40, 40, 40, 40, 1, 1, 24, 26, 26, 26, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 40, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26] 117 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450713 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450713/1 /scratch/stefan/7786230/working/building/REAL300024450713 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/601 `/scratch/stefan/7786230/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C) `REAL300024450713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450713/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450713 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 3 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450713 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450713 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450713 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450713/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450713/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450713 Building REAL300024450714 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450714' /scratch/stefan/7786230/working/building/REAL300024450714 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450714 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450714/0 /scratch/stefan/7786230/working/building/REAL300024450714 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/602 `/scratch/stefan/7786230/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450714/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450714 none CCC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 129, 129, 120, 129, 120, 120, 86, 86, 86, 86, 86, 84, 27, 84, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 129, 120, 86, 86, 86, 86, 86, 86, 86, 27, 27, 1, 86, 86, 86, 86] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 835 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450714 none CCC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 6, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 86, 86, 86, 86, 86, 1, 1, 21, 21, 21, 21, 21, 11, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 225 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450714 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450714 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450714/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450714 Building REAL300024450715 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450715' /scratch/stefan/7786230/working/building/REAL300024450715 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450715 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450715/0 /scratch/stefan/7786230/working/building/REAL300024450715 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/603 `/scratch/stefan/7786230/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C3(CC3)C23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450715/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450715 none CC1C(NC(=O)C2C3(CC3)C23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 58, 102, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 58, 58, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 450 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: REAL300024450715 none CC1C(NC(=O)C2C3(CC3)C23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 96, 96, 98, 98, 98, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 50, 96, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 50, 50, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 629 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450715 none CC1C(NC(=O)C2C3(CC3)C23CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 11, 25, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 96] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450715 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450715 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450715/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450715 Building REAL300024450716 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450716' /scratch/stefan/7786230/working/building/REAL300024450716 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450716 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450716/0 /scratch/stefan/7786230/working/building/REAL300024450716 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/604 `/scratch/stefan/7786230/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450716/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450716 none CCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 140, 92, 92, 92, 83, 83, 83, 83, 83, 74, 25, 74, 12, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 140, 140, 92, 83, 83, 83, 83, 83, 83, 83, 25, 25, 1, 83, 83, 83, 83] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 817 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450716 none CCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 22, 83, 83, 83, 83, 83, 1, 1, 26, 26, 26, 26, 26, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 83, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450716 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450716 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450716/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450716 Building REAL300024450717 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450717' /scratch/stefan/7786230/working/building/REAL300024450717 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450717 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450717/0 /scratch/stefan/7786230/working/building/REAL300024450717 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/605 `/scratch/stefan/7786230/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450717/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450717 none CCC(F)(F)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 199, 156, 201, 201, 107, 107, 107, 83, 83, 83, 83, 83, 81, 29, 81, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 201, 201, 156, 156, 107, 83, 83, 83, 83, 83, 83, 83, 29, 29, 1, 83, 83, 83, 83] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 894 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450717 none CCC(F)(F)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 27, 17, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 83, 83, 83, 83, 83, 1, 1, 30, 30, 30, 30, 30, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 83, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450717 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450717 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450717/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450717 Building REAL300024450718 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450718' /scratch/stefan/7786230/working/building/REAL300024450718 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450718 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450718/0 /scratch/stefan/7786230/working/building/REAL300024450718 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/606 `/scratch/stefan/7786230/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450718/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450718 none CC1=NOC=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 37, 37, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 48, 48, 48, 48, 48, 1, 1, 37, 37, 37, 37, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 33 ./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: REAL300024450718 none CC1=NOC=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 148, 63, 63, 63, 48, 48, 48, 48, 48, 43, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 201, 201, 148, 148, 63, 48, 48, 48, 48, 48, 48, 48, 26, 26, 1, 48, 48, 48, 48] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 686 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450718 none CC1=NOC=C1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 28, 28, 28, 37, 37, 37, 37, 37, 48, 48, 85, 129, 201, 201, 201, 201, 201, 37, 37, 2, 2, 2, 1, 7, 7, 28, 37, 37, 37, 37, 37, 37, 37, 85, 85, 201, 37, 37, 37, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 8, 9, 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: 544 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450718 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450718 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450718/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450718 Building REAL300024450719 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450719' /scratch/stefan/7786230/working/building/REAL300024450719 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450719 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450719/0 /scratch/stefan/7786230/working/building/REAL300024450719 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/607 `/scratch/stefan/7786230/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450719/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450719 none CC1C(NC(=O)CC2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 24, 24, 5, 24, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 41, 41, 84, 122, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 24, 5, 5, 1, 32, 32, 32, 32, 32, 32, 84, 84, 201] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 541 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: REAL300024450719 none CC1C(NC(=O)CC2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 73, 102, 102, 102, 183, 201, 201, 201, 201, 73, 73, 73, 73, 53, 73, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 102, 183, 183, 201, 73, 73, 73, 73, 73, 73, 53, 53, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 777 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450719 none CC1C(NC(=O)CC2=CSN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 14, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 21, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 9, 15, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 3, 21, 21, 32, 1, 1, 1, 1, 1, 1, 9, 9, 73] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450719 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450719 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450719/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450719 Building REAL300024450720 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450720' /scratch/stefan/7786230/working/building/REAL300024450720 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450720 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450720/0 /scratch/stefan/7786230/working/building/REAL300024450720 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/608 `/scratch/stefan/7786230/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)NN1) `REAL300024450720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450720/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450720 none CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 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: [56, 56, 56, 56, 80, 80, 80, 196, 201, 201, 56, 56, 56, 53, 26, 53, 11, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 80, 196, 196, 56, 56, 56, 56, 56, 56, 26, 26, 1, 1] 201 rigid atoms, others: [40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 757 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450720 none CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 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, 6, 6, 6, 29, 59, 59, 1, 1, 1, 1, 1, 3, 3, 11, 30, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 6, 29, 29, 1, 1, 1, 1, 1, 1, 11, 11, 56, 56] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 10, 11, 12, 13, 14, 34, 35, 27, 28, 37] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 38, 39, 40, 41]) total number of confs: 250 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450720 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450720/1 /scratch/stefan/7786230/working/building/REAL300024450720 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/609 `/scratch/stefan/7786230/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)[N-]N1) `REAL300024450720.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450720/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450720 none CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)[N-]N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [18, 18, 18, 18, 36, 36, 36, 108, 118, 118, 18, 18, 18, 18, 17, 18, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 36, 108, 108, 18, 18, 18, 18, 18, 18, 17, 17, 1] 118 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 421 number of broken/clashed sets: 67 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450720 none CC1C(NC(=O)CN=[N+]=[N-])CCCN1C(=O)CSC1=NC(=O)[N-]N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 6, 6, 6, 38, 58, 58, 1, 1, 1, 1, 1, 3, 3, 5, 9, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 6, 38, 38, 1, 1, 1, 1, 1, 1, 5, 5, 18] 118 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 10, 11, 12, 13, 14, 34, 35, 27, 28, 37] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450720 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450720 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450720/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450720/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450720 Building REAL300024450721 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450721' /scratch/stefan/7786230/working/building/REAL300024450721 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450721 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450721/0 /scratch/stefan/7786230/working/building/REAL300024450721 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/610 `/scratch/stefan/7786230/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450721/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450721 none CC1C(NC(=O)C2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 17, 17, 54, 125, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 54, 54, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 440 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: REAL300024450721 none CC1C(NC(=O)C2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [126, 126, 126, 126, 142, 142, 142, 201, 201, 201, 201, 201, 126, 126, 126, 126, 58, 126, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 142, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 58, 58, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 639 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450721 none CC1C(NC(=O)C2CCC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 10, 34, 126, 126, 126, 126, 126, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 126] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450721 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450721 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450721/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450721 Building REAL300024450722 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450722' /scratch/stefan/7786230/working/building/REAL300024450722 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450722 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450722/0 /scratch/stefan/7786230/working/building/REAL300024450722 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/611 `/scratch/stefan/7786230/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450722/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450722 none CC1C(NC(=O)C(C)(C)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 117, 117, 117, 201, 201, 201, 201, 68, 68, 68, 67, 47, 67, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 117, 201, 201, 201, 201, 201, 201, 201, 201, 603, 68, 68, 68, 68, 68, 68, 47, 47, 1] 603 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 1388 number of broken/clashed sets: 189 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450722 none CC1C(NC(=O)C(C)(C)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 33, 1, 1, 1, 1, 1, 3, 3, 11, 20, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 6, 18, 18, 18, 18, 18, 18, 33, 33, 99, 1, 1, 1, 1, 1, 1, 11, 11, 68] 603 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 351 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450722 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450722 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450722/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450722 Building REAL300024450723 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450723' /scratch/stefan/7786230/working/building/REAL300024450723 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450723 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450723/0 /scratch/stefan/7786230/working/building/REAL300024450723 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/612 `/scratch/stefan/7786230/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CN1N=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450723/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450723 none C=CN1N=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 14, 14, 14, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 34, 126, 126, 126, 126, 126, 1, 1, 17, 17, 17, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 126, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 40 ./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: REAL300024450723 none C=CN1N=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 144, 144, 144, 126, 126, 126, 126, 126, 108, 33, 108, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 144, 126, 126, 126, 126, 126, 126, 126, 33, 33, 1, 126, 126, 126, 126] 201 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 523 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450723 none C=CN1N=CC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 14, 14, 14, 14, 14, 26, 26, 76, 125, 201, 201, 201, 201, 201, 14, 14, 4, 4, 4, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 76, 76, 201, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 505 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450723 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450723 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450723/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450723 Building REAL300024450724 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450724' /scratch/stefan/7786230/working/building/REAL300024450724 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450724 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450724/0 /scratch/stefan/7786230/working/building/REAL300024450724 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/613 `/scratch/stefan/7786230/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450724/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450724 none CC1C(NC(=O)C2=NC=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 48, 112, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 3, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 48, 48, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 430 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: REAL300024450724 none CC1C(NC(=O)C2=NC=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [153, 153, 153, 153, 191, 191, 191, 201, 201, 201, 201, 201, 153, 153, 153, 148, 60, 148, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 191, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 153, 60, 60, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 625 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450724 none CC1C(NC(=O)C2=NC=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 15, 49, 153, 153, 153, 153, 153, 2, 2, 2, 1, 1, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 15, 15, 153] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450724 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450724 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450724/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450724 Building REAL300024450725 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450725' /scratch/stefan/7786230/working/building/REAL300024450725 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450725 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450725/0 /scratch/stefan/7786230/working/building/REAL300024450725 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/614 `/scratch/stefan/7786230/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450725/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450725 none CC1C(NC(=O)CC(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 30, 30, 9, 30, 4, 1, 4, 1, 1, 1, 32, 32, 32, 32, 32, 49, 49, 98, 141, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 30, 9, 9, 4, 12, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 98, 98, 201] 603 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 592 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: REAL300024450725 none CC1C(NC(=O)CC(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 87, 87, 87, 92, 92, 92, 178, 195, 195, 201, 201, 87, 87, 87, 78, 26, 78, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 92, 178, 178, 195, 585, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 87, 26, 26, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1352 number of broken/clashed sets: 48 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450725 none CC1C(NC(=O)CC(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 19, 19, 32, 32, 1, 1, 1, 1, 1, 3, 3, 12, 24, 87, 87, 87, 87, 87, 2, 2, 2, 1, 1, 3, 12, 12, 19, 57, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 12, 12, 87] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 328 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450725 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450725 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450725/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450725 Building REAL300024450726 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450726' /scratch/stefan/7786230/working/building/REAL300024450726 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450726 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450726/0 /scratch/stefan/7786230/working/building/REAL300024450726 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/615 `/scratch/stefan/7786230/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450726/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450726 none CC(C)CC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 100, 193, 100, 100, 80, 80, 80, 80, 80, 73, 27, 73, 12, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 100, 80, 80, 80, 80, 80, 80, 80, 27, 27, 1, 80, 80, 80, 80] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 754 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450726 none CC(C)CC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 14, 3, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 80, 80, 80, 80, 80, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 80, 1, 2, 2, 2] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450726 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450726 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450726/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450726 Building REAL300024450727 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450727' /scratch/stefan/7786230/working/building/REAL300024450727 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450727 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450727/0 /scratch/stefan/7786230/working/building/REAL300024450727 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/616 `/scratch/stefan/7786230/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C#CC2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450727/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450727 none CC1C(NC(=O)C#CC2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 48, 108, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 48, 48, 201] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 38, 39, 37] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 422 number of broken/clashed sets: 23 ./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: REAL300024450727 none CC1C(NC(=O)C#CC2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 152, 64, 152, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 159, 64, 64, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 627 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450727 none CC1C(NC(=O)C#CC2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 15, 50, 159, 159, 159, 159, 159, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 15, 15, 159] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 262 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450727 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450727 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450727/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450727 Building REAL300024450728 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450728' /scratch/stefan/7786230/working/building/REAL300024450728 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450728 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450728/0 /scratch/stefan/7786230/working/building/REAL300024450728 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/617 `/scratch/stefan/7786230/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450728/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450728 none CC(=CC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 3, 17, 17, 31, 31, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 84, 84, 84, 84, 84, 1, 1, 17, 17, 17, 17, 31, 31, 31, 31, 31, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 84, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 27 ./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: REAL300024450728 none CC(=CC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 91, 174, 174, 201, 201, 91, 91, 84, 84, 84, 84, 84, 73, 27, 73, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 174, 174, 174, 174, 201, 201, 201, 201, 201, 91, 84, 84, 84, 84, 84, 84, 84, 27, 27, 1, 84, 84, 84, 84] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 639 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450728 none CC(=CC1CC1)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 4, 21, 21, 21, 31, 31, 31, 31, 31, 43, 43, 92, 135, 201, 201, 201, 201, 201, 31, 31, 4, 4, 4, 4, 1, 1, 1, 1, 1, 21, 31, 31, 31, 31, 31, 31, 31, 92, 92, 201, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 34, 30, 31] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 549 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450728 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450728 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450728/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450728 Building REAL300024450729 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450729' /scratch/stefan/7786230/working/building/REAL300024450729 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450729 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450729/0 /scratch/stefan/7786230/working/building/REAL300024450729 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/618 `/scratch/stefan/7786230/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450729/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450729 none CC1C(NC(=O)C=CC2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 25, 25, 7, 24, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 41, 41, 82, 108, 170, 170, 170, 170, 170, 29, 29, 29, 29, 29, 25, 7, 7, 1, 1, 29, 29, 29, 29, 29, 29, 82, 82, 170] 170 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 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, 44, 45]) total number of confs: 456 number of broken/clashed sets: 24 ./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: REAL300024450729 none CC1C(NC(=O)C=CC2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 109, 109, 109, 156, 156, 170, 170, 170, 170, 100, 100, 100, 95, 41, 95, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 109, 156, 156, 170, 170, 100, 100, 100, 100, 100, 100, 41, 41, 1] 170 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450729 none CC1C(NC(=O)C=CC2=COC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 12, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 14, 14, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 15, 28, 100, 100, 100, 100, 100, 2, 2, 2, 1, 1, 3, 14, 14, 29, 29, 1, 1, 1, 1, 1, 1, 15, 15, 100] 170 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 225 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450729 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450729 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450729/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450729 Building REAL300024450730 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450730' /scratch/stefan/7786230/working/building/REAL300024450730 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450730 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450730/0 /scratch/stefan/7786230/working/building/REAL300024450730 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/619 `/scratch/stefan/7786230/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450730/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450730 none CC1C(NC(=O)CC2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 22, 22, 6, 22, 1, 1, 1, 6, 1, 1, 1, 31, 31, 31, 31, 31, 44, 44, 80, 124, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 22, 6, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 80, 80, 201] 603 rigid atoms, others: [43, 38, 6, 7, 8, 41, 10, 11, 12, 40, 39, 42] set([0, 1, 2, 3, 4, 5, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 549 number of broken/clashed sets: 46 ./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: REAL300024450730 none CC1C(NC(=O)CC2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 81, 81, 81, 95, 95, 95, 183, 201, 201, 201, 201, 201, 81, 81, 81, 78, 27, 78, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 95, 183, 183, 201, 201, 603, 201, 201, 201, 201, 201, 201, 81, 81, 81, 81, 81, 81, 27, 27, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1347 number of broken/clashed sets: 46 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450730 none CC1C(NC(=O)CC2(CO)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 17, 31, 34, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 10, 22, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 6, 17, 17, 34, 34, 102, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 10, 10, 81] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 350 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450730 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450730 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450730/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450730 Building REAL300024450731 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450731' /scratch/stefan/7786230/working/building/REAL300024450731 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450731 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450731/0 /scratch/stefan/7786230/working/building/REAL300024450731 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/620 `/scratch/stefan/7786230/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NC=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450731/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450731 none CC1C(NC(=O)CC2=NC=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 25, 25, 4, 25, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 47, 47, 88, 128, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 25, 4, 4, 1, 1, 33, 33, 33, 33, 33, 33, 88, 88, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 number of broken/clashed sets: 8 ./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: REAL300024450731 none CC1C(NC(=O)CC2=NC=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [82, 82, 82, 82, 105, 105, 105, 177, 201, 201, 201, 201, 82, 82, 82, 77, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 105, 177, 177, 201, 201, 82, 82, 82, 82, 82, 82, 30, 30, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 745 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450731 none CC1C(NC(=O)CC2=NC=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 8, 1, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 10, 16, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 4, 20, 20, 33, 33, 1, 1, 1, 1, 1, 1, 10, 10, 82] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450731 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450731 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450731/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450731 Building REAL300024450732 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450732' /scratch/stefan/7786230/working/building/REAL300024450732 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450732 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450732/0 /scratch/stefan/7786230/working/building/REAL300024450732 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/621 `/scratch/stefan/7786230/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450732/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450732 none CC1C(NC(=O)C2CCC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 25, 25, 87, 131, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 13, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 87, 87, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 36 ./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: REAL300024450732 none CC1C(NC(=O)C2CCC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 106, 106, 106, 119, 119, 119, 201, 201, 201, 201, 201, 106, 106, 106, 99, 41, 99, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 119, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 106, 41, 41, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 624 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450732 none CC1C(NC(=O)C2CCC=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 15, 31, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 15, 15, 106] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450732 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450732 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450732/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450732 Building REAL300024450733 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450733' /scratch/stefan/7786230/working/building/REAL300024450733 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450733 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450733/0 /scratch/stefan/7786230/working/building/REAL300024450733 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/622 `/scratch/stefan/7786230/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450733/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450733 none CC1C(NC(=O)C(C)(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 9, 9, 3, 9, 1, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 14, 25, 25, 85, 134, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 9, 3, 3, 3, 9, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 85, 85, 201] 603 rigid atoms, others: [43, 37, 6, 39, 40, 9, 10, 11, 12, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 540 number of broken/clashed sets: 247 ./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: REAL300024450733 none CC1C(NC(=O)C(C)(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [138, 138, 138, 138, 158, 158, 158, 201, 201, 201, 201, 201, 201, 138, 138, 138, 124, 31, 124, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 158, 201, 201, 201, 603, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 31, 31, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1274 number of broken/clashed sets: 247 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450733 none CC1C(NC(=O)C(C)(O)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 13, 31, 138, 138, 138, 138, 138, 2, 2, 2, 1, 1, 3, 11, 11, 11, 33, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 13, 13, 138] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 292 number of broken/clashed sets: 247 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450733 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450733 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450733/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450733 Building REAL300024450734 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450734' /scratch/stefan/7786230/working/building/REAL300024450734 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450734 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450734/0 /scratch/stefan/7786230/working/building/REAL300024450734 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/623 `/scratch/stefan/7786230/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450734/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450734 none CC1C(NC(=O)C2CCC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 21, 21, 72, 99, 156, 156, 156, 156, 156, 13, 13, 13, 13, 13, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 72, 72, 156] 156 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 424 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: REAL300024450734 none CC1C(NC(=O)C2CCC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 92, 107, 107, 107, 156, 156, 156, 156, 156, 156, 92, 92, 92, 87, 41, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 107, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 92, 92, 92, 92, 92, 92, 41, 41, 1] 156 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 510 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450734 none CC1C(NC(=O)C2CCC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 15, 31, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 15, 15, 92] 156 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450734 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450734 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450734/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450734 Building REAL300024450735 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450735' /scratch/stefan/7786230/working/building/REAL300024450735 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450735 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450735/0 /scratch/stefan/7786230/working/building/REAL300024450735 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/624 `/scratch/stefan/7786230/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450735/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450735 none CC1C(NC(=O)CC2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 38, 38, 83, 127, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 20, 5, 5, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27, 27, 83, 83, 201] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47, 48]) total number of confs: 529 number of broken/clashed sets: 24 ./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: REAL300024450735 none CC1C(NC(=O)CC2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 74, 74, 74, 161, 201, 201, 201, 201, 201, 66, 66, 66, 61, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 74, 161, 161, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 26, 26, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 688 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450735 none CC1C(NC(=O)CC2=CC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 11, 21, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 3, 15, 15, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 11, 11, 66] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450735 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450735 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450735/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450735 Building REAL300024450736 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450736' /scratch/stefan/7786230/working/building/REAL300024450736 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450736 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450736/0 /scratch/stefan/7786230/working/building/REAL300024450736 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/625 `/scratch/stefan/7786230/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450736/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450736 none CC1C(NC(=O)CC2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 26, 26, 6, 26, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 50, 50, 93, 125, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 26, 6, 6, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 93, 93, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 39 ./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: REAL300024450736 none CC1C(NC(=O)CC2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 88, 88, 88, 149, 201, 201, 201, 70, 70, 70, 70, 49, 70, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 88, 149, 149, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 49, 49, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 854 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450736 none CC1C(NC(=O)CC2CSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 20, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 10, 16, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 5, 20, 20, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 10, 10, 70] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450736 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450736 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450736/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450736 Building REAL300024450737 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450737' /scratch/stefan/7786230/working/building/REAL300024450737 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450737 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450737/0 /scratch/stefan/7786230/working/building/REAL300024450737 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/626 `/scratch/stefan/7786230/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(F)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450737/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450737 none CC1C(NC(=O)C2(F)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 21, 21, 60, 120, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 60, 60, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 467 number of broken/clashed sets: 14 ./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: REAL300024450737 none CC1C(NC(=O)C2(F)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 97, 97, 97, 109, 109, 109, 201, 201, 201, 201, 97, 97, 97, 96, 47, 96, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 109, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97, 97, 97, 47, 47, 1] 201 rigid atoms, others: [45, 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, 43, 44]) total number of confs: 652 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450737 none CC1C(NC(=O)C2(F)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 12, 32, 97, 97, 97, 97, 97, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 97] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450737 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450737 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450737/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450737 Building REAL300024450738 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450738' /scratch/stefan/7786230/working/building/REAL300024450738 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450738 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450738/0 /scratch/stefan/7786230/working/building/REAL300024450738 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/627 `/scratch/stefan/7786230/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450738/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450738 none CC1C(NC(=O)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 174, 174, 174, 201, 201, 201, 201, 174, 174, 174, 165, 65, 165, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 201, 201, 201, 603, 174, 174, 174, 174, 174, 174, 65, 65, 1] 603 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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]) total number of confs: 1215 number of broken/clashed sets: 75 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450738 none CC1C(NC(=O)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 17, 1, 1, 1, 1, 1, 4, 4, 16, 52, 174, 174, 174, 174, 174, 2, 2, 2, 1, 1, 6, 17, 17, 51, 1, 1, 1, 1, 1, 1, 16, 16, 174] 603 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 8, 9, 10, 11, 12, 34, 35, 25, 26, 31] set([4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 378 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450738 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450738 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450738/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450738 Building REAL300024450739 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450739' /scratch/stefan/7786230/working/building/REAL300024450739 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450739 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450739/0 /scratch/stefan/7786230/working/building/REAL300024450739 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/628 `/scratch/stefan/7786230/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450739/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450739 none CC1C(NC(=O)C=CC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 49, 49, 49, 53, 53, 53, 77, 77, 88, 88, 49, 49, 49, 48, 31, 48, 13, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 53, 77, 77, 88, 88, 49, 49, 49, 49, 49, 49, 31, 31, 1] 88 rigid atoms, others: [43, 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: 309 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450739 none CC1C(NC(=O)C=CC(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 11, 11, 23, 23, 1, 1, 1, 1, 1, 3, 3, 10, 20, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 3, 11, 11, 23, 23, 1, 1, 1, 1, 1, 1, 10, 10, 49] 88 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 165 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450739 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450739 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450739/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450739 Building REAL300024450740 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450740' /scratch/stefan/7786230/working/building/REAL300024450740 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450740 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450740/0 /scratch/stefan/7786230/working/building/REAL300024450740 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/629 `/scratch/stefan/7786230/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C[N+]([O-])=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450740/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450740 none CC1C(NC(=O)C2=CC=C[N+]([O-])=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 47, 90, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 47, 47, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 425 number of broken/clashed sets: 23 ./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: REAL300024450740 none CC1C(NC(=O)C2=CC=C[N+]([O-])=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 68, 68, 68, 201, 201, 201, 201, 201, 201, 67, 67, 67, 65, 35, 65, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 68, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 35, 35, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 404 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450740 none CC1C(NC(=O)C2=CC=C[N+]([O-])=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 11, 25, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 11, 11, 67] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450740 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450740 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450740/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450740 Building REAL300024450741 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450741' /scratch/stefan/7786230/working/building/REAL300024450741 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450741 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450741/0 /scratch/stefan/7786230/working/building/REAL300024450741 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/630 `/scratch/stefan/7786230/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450741/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450741 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 43, 65, 109, 109, 109, 109, 109, 7, 7, 7, 7, 7, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 43, 43, 109] 109 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 24 ./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: REAL300024450741 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 102, 102, 102, 109, 109, 109, 109, 109, 109, 84, 84, 84, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 102, 109, 109, 109, 84, 84, 84, 84, 84, 84, 39, 39, 1] 109 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 344 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450741 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 4, 4, 18, 35, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 4, 7, 7, 7, 1, 1, 1, 1, 1, 1, 18, 18, 84] 109 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450741 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450741 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450741/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450741 Building REAL300024450742 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450742' /scratch/stefan/7786230/working/building/REAL300024450742 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450742 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450742/0 /scratch/stefan/7786230/working/building/REAL300024450742 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/631 `/scratch/stefan/7786230/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450742/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450742 none C#CCSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 164, 135, 46, 46, 46, 38, 38, 38, 38, 38, 38, 22, 38, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 201, 201, 201, 135, 135, 46, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1, 38, 38, 38, 38] 201 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 791 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450742 none C#CCSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 20, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 38, 38, 38, 38, 38, 1, 1, 32, 32, 32, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 38, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450742 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450742 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450742/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450742 Building REAL300024450743 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450743' /scratch/stefan/7786230/working/building/REAL300024450743 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450743 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450743/0 /scratch/stefan/7786230/working/building/REAL300024450743 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/632 `/scratch/stefan/7786230/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450743/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450743 none CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 166, 201, 166, 166, 155, 155, 155, 155, 155, 146, 52, 146, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 603, 166, 155, 155, 155, 155, 155, 155, 155, 52, 52, 1, 155, 155, 155, 155] 603 rigid atoms, others: [38, 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, 39, 40, 41, 42]) total number of confs: 1287 number of broken/clashed sets: 60 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450743 none CC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 45, 155, 155, 155, 155, 155, 1, 1, 13, 13, 13, 13, 39, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 155, 1, 2, 2, 2] 603 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450743 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450743 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450743/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450743 Building REAL300024450744 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450744' /scratch/stefan/7786230/working/building/REAL300024450744 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450744 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450744/0 /scratch/stefan/7786230/working/building/REAL300024450744 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/633 `/scratch/stefan/7786230/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450744/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450744 none CC1C(NC(=O)C2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 23, 23, 68, 113, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 68, 68, 201] 603 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 51 ./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: REAL300024450744 none CC1C(NC(=O)C2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 95, 95, 95, 109, 109, 109, 201, 201, 201, 201, 95, 95, 95, 93, 49, 93, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 109, 603, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 95, 95, 49, 49, 1] 603 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 1265 number of broken/clashed sets: 51 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450744 none CC1C(NC(=O)C2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 31, 95, 95, 95, 95, 95, 2, 2, 2, 1, 1, 3, 42, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 95] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450744 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450744 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450744/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450744 Building REAL300024450745 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450745' /scratch/stefan/7786230/working/building/REAL300024450745 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450745 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450745/0 /scratch/stefan/7786230/working/building/REAL300024450745 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/634 `/scratch/stefan/7786230/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450745/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450745 none CC1C(NC(=O)C(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 25, 25, 6, 25, 1, 6, 1, 1, 1, 37, 37, 37, 37, 37, 52, 52, 95, 128, 201, 201, 201, 201, 201, 37, 37, 37, 37, 37, 25, 6, 18, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 95, 95, 201] 603 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 574 number of broken/clashed sets: 165 ./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: REAL300024450745 none CC1C(NC(=O)C(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 128, 128, 128, 158, 158, 201, 201, 77, 77, 77, 76, 59, 76, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 128, 158, 474, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 77, 59, 59, 1] 603 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 1221 number of broken/clashed sets: 165 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450745 none CC1C(NC(=O)C(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 21, 21, 37, 37, 1, 1, 1, 1, 1, 3, 3, 11, 21, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 6, 21, 63, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 11, 11, 77] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 316 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450745 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450745 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450745/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450745 Building REAL300024450746 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450746' /scratch/stefan/7786230/working/building/REAL300024450746 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450746 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450746/0 /scratch/stefan/7786230/working/building/REAL300024450746 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/635 `/scratch/stefan/7786230/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C(N)=O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450746/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450746 none CC1C(NC(=O)C2(C(N)=O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [35, 4, 37, 6, 7, 40, 10, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 13 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: REAL300024450746 none CC1C(NC(=O)C2(C(N)=O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450746 none CC1C(NC(=O)C2(C(N)=O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450746 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450746 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450746/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450746 Building REAL300024450747 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450747' /scratch/stefan/7786230/working/building/REAL300024450747 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450747 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450747/0 /scratch/stefan/7786230/working/building/REAL300024450747 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/636 `/scratch/stefan/7786230/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2C=NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450747/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450747 none CC1C(NC(=O)CN2C=NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 28, 28, 8, 28, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 48, 48, 95, 133, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 28, 8, 8, 1, 1, 40, 40, 40, 40, 40, 40, 95, 95, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 574 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: REAL300024450747 none CC1C(NC(=O)CN2C=NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 88, 88, 88, 201, 201, 201, 201, 201, 64, 64, 64, 64, 47, 64, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 88, 201, 201, 201, 201, 64, 64, 64, 64, 64, 64, 47, 47, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 809 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450747 none CC1C(NC(=O)CN2C=NN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 21, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 9, 15, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 4, 21, 21, 39, 39, 1, 1, 1, 1, 1, 1, 9, 9, 64] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450747 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450747 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450747/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450747 Building REAL300024450748 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450748' /scratch/stefan/7786230/working/building/REAL300024450748 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450748 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450748/0 /scratch/stefan/7786230/working/building/REAL300024450748 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/637 `/scratch/stefan/7786230/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450748/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450748 none C=CCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 149, 75, 149, 75, 75, 57, 57, 57, 57, 57, 54, 25, 54, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 149, 149, 149, 149, 75, 57, 57, 57, 57, 57, 57, 57, 25, 25, 1, 57, 57, 57, 57] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 888 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450748 none C=CCC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 21, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 57, 57, 57, 57, 57, 1, 1, 31, 31, 31, 21, 21, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 57, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450748 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450748 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450748/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450748 Building REAL300024450749 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450749' /scratch/stefan/7786230/working/building/REAL300024450749 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450749 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450749/0 /scratch/stefan/7786230/working/building/REAL300024450749 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/638 `/scratch/stefan/7786230/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450749/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450749 none CC1C(NC(=O)C2CC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 1, 12, 1, 1, 1, 1, 18, 18, 18, 18, 18, 25, 25, 69, 117, 201, 201, 201, 201, 201, 18, 18, 18, 18, 18, 12, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 69, 69, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 483 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: REAL300024450749 none CC1C(NC(=O)C2CC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 96, 96, 96, 124, 124, 124, 201, 201, 201, 96, 96, 96, 95, 46, 95, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 124, 201, 201, 201, 201, 96, 96, 96, 96, 96, 96, 46, 46, 1] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 657 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450749 none CC1C(NC(=O)C2CC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 11, 26, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 4, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 11, 11, 96] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 10, 11, 12, 13, 14, 34, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450749 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450749 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450749/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450749 Building REAL300024450750 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450750' /scratch/stefan/7786230/working/building/REAL300024450750 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450750 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450750/0 /scratch/stefan/7786230/working/building/REAL300024450750 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/639 `/scratch/stefan/7786230/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COC2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450750/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450750 none CC1C(NC(=O)COC2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 31, 31, 10, 31, 6, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 62, 62, 119, 153, 201, 201, 201, 201, 201, 41, 41, 41, 41, 41, 31, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 119, 119, 201] 201 rigid atoms, others: [43, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 633 number of broken/clashed sets: 6 ./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: REAL300024450750 none CC1C(NC(=O)COC2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 78, 78, 97, 97, 97, 149, 186, 201, 201, 201, 201, 78, 78, 78, 73, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 97, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 78, 31, 31, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 712 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450750 none CC1C(NC(=O)COC2(C)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 22, 41, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 10, 18, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 3, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 10, 10, 78] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 246 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450750 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450750 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450750/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450750 Building REAL300024450751 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450751' /scratch/stefan/7786230/working/building/REAL300024450751 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450751 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450751/0 /scratch/stefan/7786230/working/building/REAL300024450751 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/640 `/scratch/stefan/7786230/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450751/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450751 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 82, 117, 82, 82, 40, 40, 40, 40, 40, 40, 29, 40, 12, 1, 1, 1, 1, 1, 1, 1, 40, 40, 117, 117, 117, 117, 117, 117, 117, 82, 40, 40, 40, 40, 40, 40, 40, 29, 29, 1, 40, 40, 40, 40, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 434 number of broken/clashed sets: 109 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450751 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 40, 40, 40, 40, 40, 1, 1, 24, 26, 26, 26, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 40, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26] 117 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450751 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450751/1 /scratch/stefan/7786230/working/building/REAL300024450751 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/641 `/scratch/stefan/7786230/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C) `REAL300024450751.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450751/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450751 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 3 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450751 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450751 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450751 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450751/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450751/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450751 Building REAL300024450752 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450752' /scratch/stefan/7786230/working/building/REAL300024450752 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450752 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450752/0 /scratch/stefan/7786230/working/building/REAL300024450752 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/642 `/scratch/stefan/7786230/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450752/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450752 none CC1C(NC(=O)CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 78, 78, 107, 107, 107, 201, 201, 78, 78, 78, 77, 57, 77, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 107, 201, 201, 201, 201, 78, 78, 78, 78, 78, 78, 57, 57, 1] 201 rigid atoms, others: [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, 37, 38, 39, 40]) total number of confs: 802 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450752 none CC1C(NC(=O)CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 24, 34, 1, 1, 1, 1, 1, 3, 3, 10, 17, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 5, 24, 24, 34, 34, 1, 1, 1, 1, 1, 1, 10, 10, 78] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 9, 10, 11, 12, 34, 13, 35, 26, 27] set([4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 260 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450752 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450752 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450752/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450752 Building REAL300024450753 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450753' /scratch/stefan/7786230/working/building/REAL300024450753 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450753 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450753/0 /scratch/stefan/7786230/working/building/REAL300024450753 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/643 `/scratch/stefan/7786230/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450753/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450753 none CC1C(NC(=O)CN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 23, 23, 8, 23, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 48, 48, 93, 136, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 23, 8, 8, 1, 1, 33, 33, 33, 33, 33, 33, 93, 93, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 570 number of broken/clashed sets: 6 ./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: REAL300024450753 none CC1C(NC(=O)CN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 120, 120, 120, 195, 201, 201, 201, 201, 89, 89, 89, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 120, 195, 195, 201, 201, 89, 89, 89, 89, 89, 89, 30, 30, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 783 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450753 none CC1C(NC(=O)CN2C=CN=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 19, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 10, 17, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 4, 19, 19, 33, 33, 1, 1, 1, 1, 1, 1, 10, 10, 89] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450753 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450753 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450753/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450753 Building REAL300024450754 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450754' /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450754 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450754/0 /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/644 `/scratch/stefan/7786230/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450754/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 45, 57, 79, 79, 79, 79, 79, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 45, 45, 79] 79 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 254 number of broken/clashed sets: 20 ./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: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 68, 68, 68, 79, 79, 79, 79, 79, 79, 79, 79, 42, 42, 42, 42, 26, 42, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 68, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 42, 42, 42, 42, 42, 42, 26, 26, 1] 79 rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 271 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 9, 16, 42, 42, 42, 42, 42, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 42] 79 rigid atoms, others: [0, 1, 2, 3, 48, 33, 19, 32, 50, 46, 15, 16, 17, 18, 51, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450754/1 /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/645 `/scratch/stefan/7786230/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450754.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450754/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 25, 34, 42, 42, 42, 42, 42, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 25, 25, 42] 42 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 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: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 29, 29, 29, 42, 42, 42, 42, 42, 42, 42, 42, 25, 25, 25, 25, 19, 25, 12, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 29, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 25, 25, 25, 25, 25, 19, 19, 1] 42 rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 140 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 25] 42 rigid atoms, others: [0, 1, 2, 3, 48, 33, 19, 32, 50, 46, 15, 16, 17, 18, 51, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450754/2 /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/646 `/scratch/stefan/7786230/working/3D/646' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450754.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450754/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 29, 52, 87, 87, 87, 87, 87, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 29, 29, 87] 87 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 210 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: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 72, 72, 72, 87, 87, 87, 87, 87, 87, 87, 71, 71, 71, 68, 36, 68, 12, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 72, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 71, 71, 71, 71, 71, 71, 36, 36, 1] 87 rigid atoms, others: [21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 300 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450754 none CC1C(NC(=O)[C@H]2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 16, 33, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 16, 71] 87 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 45, 14, 15, 16, 17, 50, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450754 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450754 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450754/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450754/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450754/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450754 Building REAL300024450755 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450755' /scratch/stefan/7786230/working/building/REAL300024450755 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450755 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450755/0 /scratch/stefan/7786230/working/building/REAL300024450755 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/647 `/scratch/stefan/7786230/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450755/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450755 none C=CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 21 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: REAL300024450755 none C=CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 11 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450755 none C=CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450755 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450755 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450755/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450755 Building REAL300024450756 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450756' /scratch/stefan/7786230/working/building/REAL300024450756 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450756 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450756/0 /scratch/stefan/7786230/working/building/REAL300024450756 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/648 `/scratch/stefan/7786230/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(O)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450756/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450756 none CC1C(NC(=O)C2(O)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 63, 124, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 9, 6, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 63, 63, 201] 603 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 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: 473 number of broken/clashed sets: 39 ./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: REAL300024450756 none CC1C(NC(=O)C2(O)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [128, 128, 128, 128, 146, 146, 146, 201, 201, 201, 201, 128, 128, 128, 126, 57, 126, 13, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 146, 603, 201, 201, 201, 201, 128, 128, 128, 128, 128, 128, 57, 57, 1] 603 rigid atoms, others: [44, 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, 43]) total number of confs: 1253 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450756 none CC1C(NC(=O)C2(O)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 14, 38, 128, 128, 128, 128, 128, 2, 2, 2, 1, 1, 3, 39, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 14, 14, 128] 603 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450756 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450756 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450756/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450756 Building REAL300024450757 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450757' /scratch/stefan/7786230/working/building/REAL300024450757 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450757 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450757/0 /scratch/stefan/7786230/working/building/REAL300024450757 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/649 `/scratch/stefan/7786230/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450757/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450757 none CCC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 178, 201, 89, 178, 89, 89, 76, 76, 76, 76, 76, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 534, 89, 76, 76, 76, 76, 76, 76, 76, 28, 28, 1, 76, 76, 76, 76] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1326 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450757 none CCC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 20, 12, 21, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 76, 76, 76, 76, 76, 1, 1, 22, 22, 22, 22, 22, 21, 21, 21, 21, 12, 36, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 76, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 265 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450757 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450757 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450757/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450757 Building REAL300024450758 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450758' /scratch/stefan/7786230/working/building/REAL300024450758 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450758 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450758/0 /scratch/stefan/7786230/working/building/REAL300024450758 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/650 `/scratch/stefan/7786230/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CC1) `REAL300024450758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450758/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450758 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 122, 122, 122, 116, 116, 116, 116, 116, 114, 52, 114, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 122, 116, 116, 116, 116, 116, 116, 116, 52, 52, 1, 116, 116, 116, 116, 201, 201, 201, 201] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 633 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: REAL300024450758 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 9, 12, 12, 12, 12, 12, 21, 21, 62, 116, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 2, 2, 2, 9, 12, 12, 12, 12, 12, 12, 12, 62, 62, 201, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 22, 23, 24] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 482 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450758 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 34, 116, 116, 116, 116, 116, 1, 1, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 116, 1, 2, 2, 2, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450758 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450758 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450758/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450758 Building REAL300024450759 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450759' /scratch/stefan/7786230/working/building/REAL300024450759 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450759 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450759/0 /scratch/stefan/7786230/working/building/REAL300024450759 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/651 `/scratch/stefan/7786230/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NN=N1) `REAL300024450759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450759/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450759 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.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, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [198, 114, 198, 114, 114, 70, 70, 70, 70, 70, 68, 56, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 198, 201, 201, 201, 201, 198, 198, 198, 114, 70, 70, 70, 70, 70, 70, 70, 56, 56, 1, 70, 70, 70, 70, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46]) total number of confs: 788 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: REAL300024450759 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.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, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 35, 35, 35, 62, 62, 62, 62, 62, 78, 78, 119, 151, 201, 201, 201, 201, 201, 62, 62, 1, 1, 1, 1, 1, 11, 11, 11, 35, 62, 62, 62, 62, 62, 62, 62, 119, 119, 201, 62, 62, 62, 62, 1] 201 rigid atoms, others: [1, 46, 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]) total number of confs: 609 number of broken/clashed sets: 69 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450759 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.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, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 6, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 70, 70, 70, 70, 70, 1, 1, 31, 62, 62, 62, 62, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 70, 1, 2, 2, 2, 62] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 263 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450759 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450759 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450759/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450759 Building REAL300024450760 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450760' /scratch/stefan/7786230/working/building/REAL300024450760 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450760 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450760/0 /scratch/stefan/7786230/working/building/REAL300024450760 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/652 `/scratch/stefan/7786230/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCN2N=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450760/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450760 none CC1C(NC(=O)C2CCCN2N=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 6] 6 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 19 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: REAL300024450760 none CC1C(NC(=O)C2CCCN2N=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 1] 6 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 10 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450760 none CC1C(NC(=O)C2CCCN2N=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5] 6 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450760 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450760 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450760/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450760 Building REAL300024450761 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450761' /scratch/stefan/7786230/working/building/REAL300024450761 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450761 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450761/0 /scratch/stefan/7786230/working/building/REAL300024450761 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/653 `/scratch/stefan/7786230/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450761/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450761 none CCC1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 23, 88, 88, 88, 88, 88, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 88, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 44 ./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: REAL300024450761 none CCC1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 136, 136, 136, 88, 88, 88, 88, 88, 81, 40, 81, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 88, 88, 88, 88, 88, 88, 88, 40, 40, 1, 88, 88, 88, 88] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 699 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450761 none CCC1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 24, 24, 36, 36, 93, 129, 201, 201, 201, 201, 201, 24, 24, 2, 2, 2, 2, 2, 1, 1, 1, 1, 9, 24, 24, 24, 24, 24, 24, 24, 93, 93, 201, 24, 24, 24, 24] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 30, 31] set([0, 6, 7, 8, 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, 48]) total number of confs: 563 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450761 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450761 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450761/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450761 Building REAL300024450762 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450762' /scratch/stefan/7786230/working/building/REAL300024450762 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450762 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450762/0 /scratch/stefan/7786230/working/building/REAL300024450762 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/654 `/scratch/stefan/7786230/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450762/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450762 none CC(O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [175, 187, 201, 160, 145, 51, 51, 51, 46, 46, 46, 46, 46, 46, 23, 46, 11, 1, 1, 1, 1, 1, 1, 1, 46, 46, 201, 201, 201, 201, 603, 187, 187, 186, 186, 145, 145, 51, 46, 46, 46, 46, 46, 46, 46, 23, 23, 1, 46, 46, 46, 46] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1816 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450762 none CC(O)CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 23, 35, 19, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 46, 46, 46, 46, 46, 1, 1, 35, 35, 35, 35, 105, 23, 23, 22, 22, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450762 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450762 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450762/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450762 Building REAL300024450763 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450763' /scratch/stefan/7786230/working/building/REAL300024450763 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450763 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450763/0 /scratch/stefan/7786230/working/building/REAL300024450763 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/655 `/scratch/stefan/7786230/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450763/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450763 none CC1=NOC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 67, 67, 67, 67, 67, 1, 1, 43, 43, 43, 43, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 67, 1, 2, 2, 2, 43] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 202 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: REAL300024450763 none CC1=NOC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 163, 69, 69, 69, 67, 67, 67, 67, 67, 62, 25, 62, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 163, 163, 69, 67, 67, 67, 67, 67, 67, 67, 25, 25, 1, 67, 67, 67, 67, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 642 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450763 none CC1=NOC(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 40, 40, 40, 43, 43, 43, 43, 43, 49, 49, 78, 120, 201, 201, 201, 201, 201, 43, 43, 1, 2, 2, 2, 8, 8, 40, 43, 43, 43, 43, 43, 43, 43, 78, 78, 201, 43, 43, 43, 43, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 499 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450763 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450763 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450763/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450763 Building REAL300024450764 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450764' /scratch/stefan/7786230/working/building/REAL300024450764 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450764 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450764/0 /scratch/stefan/7786230/working/building/REAL300024450764 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/656 `/scratch/stefan/7786230/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450764/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450764 none CC1C(NC(=O)CC2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 8, 8, 3, 8, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 11, 12, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 8, 3, 3, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 11, 11, 15] 45 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 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: REAL300024450764 none CC1C(NC(=O)CC2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 15, 15, 45, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 1] 45 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450764 none CC1C(NC(=O)CC2(O)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 5, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 3, 9, 9, 27, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 5, 5, 9] 45 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 87 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450764 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450764 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450764/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450764 Building REAL300024450765 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450765' /scratch/stefan/7786230/working/building/REAL300024450765 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450765 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450765/0 /scratch/stefan/7786230/working/building/REAL300024450765 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/657 `/scratch/stefan/7786230/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C3CCOCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450765/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450765 none CC1C(NC(=O)C2C3CCOCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 31, 49, 94, 94, 94, 94, 94, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 31, 31, 94] 94 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 226 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: REAL300024450765 none CC1C(NC(=O)C2C3CCOCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 87, 87, 87, 94, 94, 94, 94, 94, 94, 83, 83, 83, 80, 42, 80, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 87, 94, 94, 94, 94, 94, 94, 94, 94, 94, 83, 83, 83, 83, 83, 83, 42, 42, 1] 94 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 317 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450765 none CC1C(NC(=O)C2C3CCOCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 14, 26, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 14, 14, 83] 94 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450765 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450765 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450765/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450765 Building REAL300024450766 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450766' /scratch/stefan/7786230/working/building/REAL300024450766 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450766 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450766/0 /scratch/stefan/7786230/working/building/REAL300024450766 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/658 `/scratch/stefan/7786230/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450766/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450766 none CC1C(NC(=O)C=CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 8, 8, 8, 9, 9, 9, 6, 6, 6, 6, 5, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 8, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 5, 5, 1] 9 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 22 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450766 none CC1C(NC(=O)C=CCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 6, 6, 7, 1, 1, 1, 1, 1, 3, 3, 4, 4, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 3, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 6] 9 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 10, 11, 12, 13, 14, 34, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450766 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450766 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450766/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450766 Building REAL300024450767 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450767' /scratch/stefan/7786230/working/building/REAL300024450767 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450767 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450767/0 /scratch/stefan/7786230/working/building/REAL300024450767 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/659 `/scratch/stefan/7786230/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450767/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450767 none CC1C(NC(=O)C(F)CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 43, 43, 12, 43, 3, 12, 1, 1, 1, 1, 50, 50, 50, 50, 50, 63, 63, 104, 144, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 43, 12, 3, 3, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 104, 104, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 575 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: REAL300024450767 none CC1C(NC(=O)C(F)CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 77, 77, 77, 151, 151, 179, 201, 201, 67, 67, 67, 65, 26, 65, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 77, 151, 179, 179, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 67, 26, 26, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 819 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450767 none CC1C(NC(=O)C(F)CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 31, 50, 50, 1, 1, 1, 1, 1, 3, 3, 9, 16, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 3, 12, 31, 31, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 9, 9, 67] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450767 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450767 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450767/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450767 Building REAL300024450768 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450768' /scratch/stefan/7786230/working/building/REAL300024450768 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450768 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450768/0 /scratch/stefan/7786230/working/building/REAL300024450768 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/660 `/scratch/stefan/7786230/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450768/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450768 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 78, 78, 78, 64, 64, 64, 64, 64, 58, 25, 58, 12, 1, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 78, 64, 64, 64, 64, 64, 64, 64, 25, 25, 1, 64, 64, 64, 64, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] 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, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 787 number of broken/clashed sets: 18 ./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: REAL300024450768 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 3, 8, 28, 28, 28, 36, 36, 36, 36, 36, 55, 55, 98, 135, 201, 201, 201, 201, 201, 36, 36, 1, 1, 1, 4, 4, 4, 4, 4, 3, 8, 8, 28, 36, 36, 36, 36, 36, 36, 36, 98, 98, 201, 36, 36, 36, 36, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 50, 51, 52, 53, 54, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 585 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450768 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 25, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 64, 64, 64, 64, 64, 1, 1, 27, 36, 36, 29, 29, 29, 29, 29, 27, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 64, 1, 2, 2, 2, 36, 36, 36, 36, 36] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 12, 46, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 288 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450768 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450768 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450768/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450768 Building REAL300024450769 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450769' /scratch/stefan/7786230/working/building/REAL300024450769 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450769 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450769/0 /scratch/stefan/7786230/working/building/REAL300024450769 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/661 `/scratch/stefan/7786230/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450769/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450769 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 12, 12, 7, 11, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 17, 17, 30, 40, 57, 57, 57, 57, 57, 13, 13, 13, 13, 13, 12, 7, 7, 1, 1, 1, 13, 13, 13, 13, 13, 13, 30, 30, 57] 57 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 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: REAL300024450769 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 17, 17, 17, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16, 15, 16, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 17, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 15, 15, 1] 20 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450769 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 9, 9, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 6, 8, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 3, 9, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 16] 20 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450769 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450769 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450769/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450769 Building REAL300024450770 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450770' /scratch/stefan/7786230/working/building/REAL300024450770 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450770 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450770/0 /scratch/stefan/7786230/working/building/REAL300024450770 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/662 `/scratch/stefan/7786230/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450770/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450770 none CNC(=O)N[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 189, 133, 189, 189, 133, 133, 112, 112, 112, 112, 112, 104, 31, 104, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 189, 189, 189, 133, 112, 112, 112, 112, 112, 112, 112, 31, 31, 1, 112, 112, 112, 112] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 739 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450770 none CNC(=O)N[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 20, 20, 20, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 31, 112, 112, 112, 112, 112, 1, 1, 28, 28, 28, 28, 20, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 112, 1, 2, 2, 2] 201 rigid atoms, others: [43, 47, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 280 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450770 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450770 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450770/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450770 Building REAL300024450771 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450771' /scratch/stefan/7786230/working/building/REAL300024450771 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450771 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450771/0 /scratch/stefan/7786230/working/building/REAL300024450771 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/663 `/scratch/stefan/7786230/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)OC) `REAL300024450771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450771/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450771 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)OC 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 191, 82, 82, 82, 63, 63, 63, 63, 63, 60, 25, 60, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 198, 201, 201, 201, 201, 201, 200, 198, 191, 191, 82, 63, 63, 63, 63, 63, 63, 63, 25, 25, 1, 63, 63, 63, 63, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 783 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450771 none CCC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)OC 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 30, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 63, 63, 63, 63, 63, 1, 1, 31, 34, 36, 36, 36, 35, 35, 31, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 1, 2, 2, 2, 34, 34, 34] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 268 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450771 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450771 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450771/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450771 Building REAL300024450772 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450772' /scratch/stefan/7786230/working/building/REAL300024450772 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450772 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450772/0 /scratch/stefan/7786230/working/building/REAL300024450772 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/664 `/scratch/stefan/7786230/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450772/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450772 none CC1C(NC(=O)C2=C(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 9, 9, 1, 9, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 57, 115, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 57, 57, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 453 number of broken/clashed sets: 9 ./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: REAL300024450772 none CC1C(NC(=O)C2=C(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [134, 134, 134, 134, 162, 162, 162, 201, 201, 201, 201, 134, 134, 134, 133, 54, 133, 13, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 162, 201, 201, 201, 201, 134, 134, 134, 134, 134, 134, 54, 54, 1] 201 rigid atoms, others: [43, 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: 595 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450772 none CC1C(NC(=O)C2=C(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 13, 42, 134, 134, 134, 134, 134, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 134] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450772 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450772 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450772/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450772 Building REAL300024450773 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450773' /scratch/stefan/7786230/working/building/REAL300024450773 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450773 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450773/0 /scratch/stefan/7786230/working/building/REAL300024450773 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/665 `/scratch/stefan/7786230/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450773/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450773 none CC1=NN=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 23, 23, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 90, 90, 90, 90, 90, 1, 1, 23, 23, 23, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 90, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 206 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: REAL300024450773 none CC1=NN=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 175, 104, 104, 104, 90, 90, 90, 90, 90, 75, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 175, 175, 104, 90, 90, 90, 90, 90, 90, 90, 29, 29, 1, 90, 90, 90, 90] 201 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 685 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450773 none CC1=NN=NN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 19, 19, 19, 23, 23, 23, 23, 23, 31, 31, 82, 120, 201, 201, 201, 201, 201, 23, 23, 2, 2, 2, 4, 4, 19, 23, 23, 23, 23, 23, 23, 23, 82, 82, 201, 23, 23, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 538 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450773 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450773 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450773/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450773 Building REAL300024450774 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450774' /scratch/stefan/7786230/working/building/REAL300024450774 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450774 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450774/0 /scratch/stefan/7786230/working/building/REAL300024450774 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/666 `/scratch/stefan/7786230/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@]23C[C@H]2[C@H](F)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450774/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450774 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](F)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 7, 5, 7, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 17, 17, 45, 91, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 45, 45, 201] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 425 number of broken/clashed sets: 18 ./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: REAL300024450774 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](F)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 7, 5, 7, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 71, 71, 71, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 39, 70, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 71, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 39, 39, 1] 201 rigid atoms, others: [46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 406 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450774 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](F)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 5, 7, 5, 7, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 10, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 24, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 70] 201 rigid atoms, others: [0, 1, 2, 3, 38, 32, 40, 41, 42, 39, 14, 15, 16, 17, 18, 43, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450774 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450774 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450774/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450774 Building REAL300024450775 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450775' /scratch/stefan/7786230/working/building/REAL300024450775 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450775 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450775/0 /scratch/stefan/7786230/working/building/REAL300024450775 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/667 `/scratch/stefan/7786230/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450775/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450775 none CC1C(NC(=O)C2=CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 25, 25, 69, 100, 160, 160, 160, 160, 160, 19, 19, 19, 19, 19, 12, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 69, 69, 160] 160 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 402 number of broken/clashed sets: 34 ./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: REAL300024450775 none CC1C(NC(=O)C2=CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 117, 117, 117, 160, 160, 160, 160, 160, 111, 111, 111, 104, 45, 104, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 117, 160, 160, 160, 160, 160, 160, 160, 111, 111, 111, 111, 111, 111, 45, 45, 1] 160 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 436 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450775 none CC1C(NC(=O)C2=CCCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 13, 28, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 13, 13, 111] 160 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450775 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450775 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450775/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450775 Building REAL300024450776 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450776' /scratch/stefan/7786230/working/building/REAL300024450776 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450776 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450776/0 /scratch/stefan/7786230/working/building/REAL300024450776 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/668 `/scratch/stefan/7786230/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450776/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450776 none CC1C(NC(=O)C2(C)CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 45, 101, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 7, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 45, 45, 201] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 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, 44, 45]) total number of confs: 422 number of broken/clashed sets: 18 ./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: REAL300024450776 none CC1C(NC(=O)C2(C)CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [111, 111, 111, 111, 118, 118, 118, 201, 201, 201, 201, 201, 111, 111, 111, 110, 55, 110, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 118, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111, 55, 55, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450776 none CC1C(NC(=O)C2(C)CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 36, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 111] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450776 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450776 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450776/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450776 Building REAL300024450777 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450777' /scratch/stefan/7786230/working/building/REAL300024450777 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450777 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450777/0 /scratch/stefan/7786230/working/building/REAL300024450777 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/669 `/scratch/stefan/7786230/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450777/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450777 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [28, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 28, 88, 88, 88, 88, 88, 1, 1, 12, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 88, 1, 2, 2, 2, 12] 200 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 254 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: REAL300024450777 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 122, 122, 122, 122, 117, 117, 117, 88, 88, 88, 88, 88, 83, 39, 83, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 122, 200, 200, 200, 200, 200, 117, 88, 88, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88, 88, 88, 122] 200 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 861 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450777 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 16, 16, 44, 64, 122, 122, 122, 122, 122, 12, 12, 1, 8, 8, 8, 8, 8, 7, 12, 12, 12, 12, 12, 12, 12, 44, 44, 122, 12, 12, 12, 12, 1] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 321 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450777 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450777 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450777/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450777 Building REAL300024450778 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450778' /scratch/stefan/7786230/working/building/REAL300024450778 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450778 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450778/0 /scratch/stefan/7786230/working/building/REAL300024450778 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/670 `/scratch/stefan/7786230/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450778/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450778 none CC1C(NC(=O)C(O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 86, 86, 86, 91, 91, 91, 91, 91, 62, 62, 62, 60, 42, 60, 12, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 86, 91, 273, 91, 91, 91, 91, 91, 91, 91, 91, 91, 62, 62, 62, 62, 62, 62, 42, 42, 1] 273 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 609 number of broken/clashed sets: 63 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450778 none CC1C(NC(=O)C(O)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 7, 7, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 11, 22, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 6, 7, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 62] 273 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450778 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450778 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450778/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450778 Building REAL300024450779 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450779' /scratch/stefan/7786230/working/building/REAL300024450779 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450779 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450779/0 /scratch/stefan/7786230/working/building/REAL300024450779 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/671 `/scratch/stefan/7786230/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCSCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450779/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450779 none CC1C(NC(=O)C2CCSCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 21, 21, 63, 112, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 63, 63, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 467 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: REAL300024450779 none CC1C(NC(=O)C2CCSCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 106, 106, 106, 201, 201, 201, 201, 201, 99, 99, 99, 98, 49, 98, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 99, 99, 99, 49, 49, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 636 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450779 none CC1C(NC(=O)C2CCSCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 12, 31, 99, 99, 99, 99, 99, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 99] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450779 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450779 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450779/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450779 Building REAL300024450780 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450780' /scratch/stefan/7786230/working/building/REAL300024450780 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450780 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450780/0 /scratch/stefan/7786230/working/building/REAL300024450780 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/672 `/scratch/stefan/7786230/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450780/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450780 none C#CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 183, 77, 77, 77, 73, 73, 73, 73, 73, 71, 38, 71, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 183, 183, 77, 73, 73, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 73, 73] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 802 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450780 none C#CCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 23, 73, 73, 73, 73, 73, 1, 1, 25, 25, 25, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 73, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450780 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450780 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450780/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450780 Building REAL300024450781 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450781' /scratch/stefan/7786230/working/building/REAL300024450781 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450781 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450781/0 /scratch/stefan/7786230/working/building/REAL300024450781 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/673 `/scratch/stefan/7786230/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450781/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450781 none CC1C(NC(=O)CN2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 24, 24, 6, 24, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 47, 47, 94, 135, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 24, 6, 6, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 94, 94, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 576 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: REAL300024450781 none CC1C(NC(=O)CN2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 107, 107, 107, 182, 201, 201, 201, 91, 91, 91, 81, 28, 81, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 107, 182, 182, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 28, 28, 1] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46]) total number of confs: 713 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450781 none CC1C(NC(=O)CN2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 12, 22, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 3, 16, 16, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 12, 12, 91] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 11, 12, 13, 14, 44, 43, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450781 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450781 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450781/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450781 Building REAL300024450782 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450782' /scratch/stefan/7786230/working/building/REAL300024450782 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450782 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450782/0 /scratch/stefan/7786230/working/building/REAL300024450782 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/674 `/scratch/stefan/7786230/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450782/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450782 none CC(C)C(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 157, 201, 157, 157, 80, 80, 80, 66, 66, 66, 66, 66, 64, 25, 64, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 157, 471, 157, 157, 80, 66, 66, 66, 66, 66, 66, 66, 25, 25, 1, 66, 66, 66, 66] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1327 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450782 none CC(C)C(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 20, 35, 13, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 66, 66, 66, 66, 66, 1, 1, 35, 35, 35, 35, 35, 35, 35, 20, 60, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 66, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 337 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450782 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450782 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450782/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450782 Building REAL300024450783 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450783' /scratch/stefan/7786230/working/building/REAL300024450783 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450783 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450783/0 /scratch/stefan/7786230/working/building/REAL300024450783 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/675 `/scratch/stefan/7786230/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(Cl)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450783/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450783 none CC1C(NC(=O)C2=C(Cl)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 23, 23, 70, 119, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 13, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 70, 70, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 489 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: REAL300024450783 none CC1C(NC(=O)C2=C(Cl)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 114, 114, 114, 201, 201, 201, 201, 201, 98, 98, 98, 97, 48, 97, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 114, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 48, 48, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 499 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450783 none CC1C(NC(=O)C2=C(Cl)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 11, 26, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 11, 11, 98] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 180 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450783 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450783 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450783/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450783 Building REAL300024450784 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450784' /scratch/stefan/7786230/working/building/REAL300024450784 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450784 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450784/0 /scratch/stefan/7786230/working/building/REAL300024450784 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/676 `/scratch/stefan/7786230/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=C1) `REAL300024450784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450784/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450784 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 84, 84, 84, 84, 84, 1, 1, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 84, 1, 2, 2, 2, 8] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 177 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: REAL300024450784 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 84, 84, 84, 84, 84, 79, 40, 79, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 100, 100, 100, 100, 100, 100, 100, 100, 84, 84, 84, 84, 84, 84, 84, 40, 40, 1, 84, 84, 84, 84, 100] 100 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 329 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450784 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 12, 12, 35, 53, 100, 100, 100, 100, 100, 8, 8, 1, 1, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 35, 35, 100, 8, 8, 8, 8, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450784 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450784 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450784/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450784 Building REAL300024450785 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450785' /scratch/stefan/7786230/working/building/REAL300024450785 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450785 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450785/0 /scratch/stefan/7786230/working/building/REAL300024450785 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/677 `/scratch/stefan/7786230/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC(=O)NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450785/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450785 none CC1C(NC(=O)CC2=CC(=O)NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 39, 39, 8, 39, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 67, 67, 91, 132, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 39, 8, 8, 1, 1, 1, 54, 54, 54, 54, 54, 54, 91, 91, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 530 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: REAL300024450785 none CC1C(NC(=O)CC2=CC(=O)NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 47, 47, 64, 64, 64, 163, 201, 201, 201, 201, 201, 47, 47, 47, 46, 25, 46, 13, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 64, 163, 163, 201, 201, 201, 47, 47, 47, 47, 47, 47, 25, 25, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 691 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450785 none CC1C(NC(=O)CC2=CC(=O)NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 21, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 3, 3, 9, 16, 47, 47, 47, 47, 47, 2, 2, 2, 1, 1, 3, 21, 21, 54, 54, 54, 1, 1, 1, 1, 1, 1, 9, 9, 47] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450785 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450785 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450785/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450785 Building REAL300024450786 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450786' /scratch/stefan/7786230/working/building/REAL300024450786 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450786 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450786/0 /scratch/stefan/7786230/working/building/REAL300024450786 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/678 `/scratch/stefan/7786230/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(O)CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450786/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450786 none CC1C(NC(=O)C(O)CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 103, 103, 103, 122, 122, 122, 201, 201, 201, 201, 201, 201, 103, 103, 103, 91, 29, 91, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 122, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 103, 29, 29, 1] 603 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1342 number of broken/clashed sets: 565 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450786 none CC1C(NC(=O)C(O)CC(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 15, 15, 22, 22, 22, 22, 1, 1, 1, 1, 1, 3, 3, 12, 27, 103, 103, 103, 103, 103, 2, 2, 2, 1, 1, 3, 15, 45, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 12, 12, 103] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 305 number of broken/clashed sets: 565 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450786 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450786 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450786/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450786 Building REAL300024450787 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450787' /scratch/stefan/7786230/working/building/REAL300024450787 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450787 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450787/0 /scratch/stefan/7786230/working/building/REAL300024450787 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/679 `/scratch/stefan/7786230/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450787/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450787 none CCCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 151, 106, 151, 151, 106, 106, 76, 76, 76, 76, 76, 74, 28, 74, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 453, 106, 76, 76, 76, 76, 76, 76, 76, 28, 28, 1, 76, 76, 76, 76] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1341 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450787 none CCCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 28, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 76, 76, 76, 76, 76, 1, 1, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 42, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 76, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 294 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450787 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450787 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450787/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450787 Building REAL300024450788 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450788' /scratch/stefan/7786230/working/building/REAL300024450788 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450788 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450788/0 /scratch/stefan/7786230/working/building/REAL300024450788 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/680 `/scratch/stefan/7786230/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450788/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450788 none CCOC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 138, 199, 199, 138, 138, 103, 103, 103, 103, 103, 96, 29, 96, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 199, 199, 199, 199, 199, 199, 138, 103, 103, 103, 103, 103, 103, 103, 29, 29, 1, 103, 103, 103, 103] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 741 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450788 none CCOC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 18, 6, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 28, 103, 103, 103, 103, 103, 1, 1, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 103, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450788 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450788 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450788/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450788 Building REAL300024450789 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450789' /scratch/stefan/7786230/working/building/REAL300024450789 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450789 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450789/0 /scratch/stefan/7786230/working/building/REAL300024450789 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/681 `/scratch/stefan/7786230/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1) `REAL300024450789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450789/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450789 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 35, 78, 78, 78, 78, 78, 1, 1, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 78, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 145 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 38 ./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: REAL300024450789 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 85, 85, 85, 78, 78, 78, 78, 78, 70, 38, 70, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 145, 145, 145, 145, 145, 145, 145, 85, 78, 78, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 78, 78, 145, 145, 145, 145, 145, 145, 145, 145] 145 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 401 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450789 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 12, 12, 44, 80, 145, 145, 145, 145, 145, 9, 9, 1, 1, 1, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 44, 44, 145, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 145 rigid atoms, others: [0, 1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450789 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450789 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450789/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450789 Building REAL300024450790 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450790' /scratch/stefan/7786230/working/building/REAL300024450790 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450790 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450790/0 /scratch/stefan/7786230/working/building/REAL300024450790 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/682 `/scratch/stefan/7786230/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=C2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450790/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 35, 35, 69, 84, 124, 124, 124, 124, 124, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 25, 25, 25, 25, 69, 69, 124] 124 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 43, 36, 38, 42] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 375 number of broken/clashed sets: 20 ./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: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 67, 67, 67, 104, 104, 104, 124, 124, 124, 124, 124, 124, 124, 67, 67, 67, 67, 37, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 104, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 67, 67, 67, 67, 67, 67, 37, 37, 1] 124 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 426 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 9, 17, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 9, 9, 67] 124 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450790 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450790/1 /scratch/stefan/7786230/working/building/REAL300024450790 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/683 `/scratch/stefan/7786230/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=C2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450790.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450790/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [28, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 41, 41, 94, 122, 168, 168, 168, 168, 168, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 94, 94, 168] 168 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 43, 36, 38, 42] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 512 number of broken/clashed sets: 27 ./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: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [71, 71, 71, 71, 120, 120, 120, 168, 168, 168, 168, 168, 168, 168, 71, 71, 71, 71, 39, 71, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 120, 168, 168, 168, 168, 168, 168, 168, 168, 168, 168, 71, 71, 71, 71, 71, 71, 39, 39, 1] 168 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 572 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450790 none CC1C(NC(=O)C=C2CC[N@@H+](C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 9, 17, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 9, 9, 71] 168 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450790 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450790 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450790/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450790/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450790 Building REAL300024450791 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450791' /scratch/stefan/7786230/working/building/REAL300024450791 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450791 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450791/0 /scratch/stefan/7786230/working/building/REAL300024450791 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/684 `/scratch/stefan/7786230/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450791/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450791 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 59, 59, 59, 59, 59, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 59, 1, 2, 2, 2] 71 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 14 ./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: REAL300024450791 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 71, 68, 68, 68, 59, 59, 59, 59, 59, 55, 32, 55, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 71, 71, 71, 71, 71, 71, 71, 71, 68, 59, 59, 59, 59, 59, 59, 59, 32, 32, 1, 59, 59, 59, 59] 71 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450791 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 9, 9, 28, 42, 71, 71, 71, 71, 71, 7, 7, 1, 2, 2, 2, 2, 2, 2, 1, 4, 7, 7, 7, 7, 7, 7, 7, 28, 28, 71, 7, 7, 7, 7] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450791 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450791 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450791/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450791 Building REAL300024450792 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450792' /scratch/stefan/7786230/working/building/REAL300024450792 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450792 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450792/0 /scratch/stefan/7786230/working/building/REAL300024450792 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/685 `/scratch/stefan/7786230/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450792/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450792 none CCOC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 110, 110, 110, 110, 110, 1, 1, 11, 11, 11, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 110, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 203 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: REAL300024450792 none CCOC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 129, 129, 129, 110, 110, 110, 110, 110, 98, 31, 98, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 200, 200, 200, 201, 201, 201, 201, 201, 129, 110, 110, 110, 110, 110, 110, 110, 31, 31, 1, 110, 110, 110, 110, 200, 200, 200, 200, 200, 200] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 646 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450792 none CCOC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 1, 1, 1, 8, 8, 8, 11, 11, 11, 11, 11, 19, 19, 61, 96, 200, 200, 200, 200, 200, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 11, 11, 11, 11, 11, 11, 11, 61, 61, 200, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450792 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450792 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450792/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450792 Building REAL300024450793 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450793' /scratch/stefan/7786230/working/building/REAL300024450793 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450793 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450793/0 /scratch/stefan/7786230/working/building/REAL300024450793 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/686 `/scratch/stefan/7786230/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450793/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450793 none C#C[C@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 4, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 35, 109, 109, 109, 109, 109, 1, 1, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 109, 1, 2, 2, 2] 182 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 39 ./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: REAL300024450793 none C#C[C@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 182, 182, 182, 182, 120, 182, 120, 120, 109, 109, 109, 109, 109, 100, 41, 100, 12, 1, 1, 1, 1, 1, 1, 1, 109, 109, 182, 182, 182, 120, 109, 109, 109, 109, 109, 109, 109, 41, 41, 1, 109, 109, 109, 109] 182 rigid atoms, others: [40, 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, 41, 42, 43, 44]) total number of confs: 616 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450793 none C#C[C@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 17, 17, 68, 106, 182, 182, 182, 182, 182, 11, 11, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 68, 68, 182, 11, 11, 11, 11] 182 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450793 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450793 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450793/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450793 Building REAL300024450794 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450794' /scratch/stefan/7786230/working/building/REAL300024450794 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450794 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450794/0 /scratch/stefan/7786230/working/building/REAL300024450794 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/687 `/scratch/stefan/7786230/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)C(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450794/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450794 none CC1C(NC(=O)C2=NN(C)C(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 26, 26, 72, 102, 164, 164, 164, 164, 164, 14, 14, 14, 14, 14, 13, 2, 2, 2, 14, 14, 14, 14, 14, 14, 72, 72, 164] 164 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 470 number of broken/clashed sets: 39 ./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: REAL300024450794 none CC1C(NC(=O)C2=NN(C)C(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 164, 164, 164, 164, 164, 164, 54, 54, 54, 51, 33, 51, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 164, 164, 164, 54, 54, 54, 54, 54, 54, 33, 33, 1] 164 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 325 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450794 none CC1C(NC(=O)C2=NN(C)C(=O)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 10, 18, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 3, 14, 14, 14, 1, 1, 1, 1, 1, 1, 10, 10, 54] 164 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450794 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450794 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450794/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450794 Building REAL300024450795 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450795' /scratch/stefan/7786230/working/building/REAL300024450795 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450795 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450795/0 /scratch/stefan/7786230/working/building/REAL300024450795 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/688 `/scratch/stefan/7786230/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(N=[N+]=[N-])CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450795/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450795 none CC1C(NC(=O)C2(N=[N+]=[N-])CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 11, 11, 1, 11, 1, 1, 10, 10, 1, 1, 32, 32, 32, 32, 32, 44, 44, 81, 115, 185, 185, 185, 185, 185, 32, 32, 32, 32, 32, 11, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 81, 81, 185] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 10, 11] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 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: 500 number of broken/clashed sets: 80 ./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: REAL300024450795 none CC1C(NC(=O)C2(N=[N+]=[N-])CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 53, 53, 86, 86, 86, 185, 201, 201, 185, 185, 53, 53, 53, 50, 39, 50, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 86, 185, 185, 185, 185, 53, 53, 53, 53, 53, 53, 39, 39, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 622 number of broken/clashed sets: 80 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450795 none CC1C(NC(=O)C2(N=[N+]=[N-])CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 32, 67, 67, 32, 32, 1, 1, 1, 1, 1, 3, 3, 9, 16, 53, 53, 53, 53, 53, 2, 2, 2, 1, 1, 6, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 9, 9, 53] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450795 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450795 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450795/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450795 Building REAL300024450796 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450796' /scratch/stefan/7786230/working/building/REAL300024450796 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450796 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450796/0 /scratch/stefan/7786230/working/building/REAL300024450796 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/689 `/scratch/stefan/7786230/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CNC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450796/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450796 none CC1C(NC(=O)C2=CNC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 58, 119, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 1, 11, 11, 11, 11, 11, 11, 58, 58, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 440 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: REAL300024450796 none CC1C(NC(=O)C2=CNC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [184, 184, 184, 184, 186, 186, 186, 201, 201, 201, 201, 201, 184, 184, 184, 182, 70, 182, 13, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 186, 201, 201, 184, 184, 184, 184, 184, 184, 70, 70, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 579 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450796 none CC1C(NC(=O)C2=CNC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 15, 53, 184, 184, 184, 184, 184, 2, 2, 2, 1, 1, 4, 11, 11, 1, 1, 1, 1, 1, 1, 15, 15, 184] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 296 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450796 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450796 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450796/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450796 Building REAL300024450797 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450797' /scratch/stefan/7786230/working/building/REAL300024450797 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450797 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450797/0 /scratch/stefan/7786230/working/building/REAL300024450797 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/690 `/scratch/stefan/7786230/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450797/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450797 none CC(C)[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 19, 31, 19, 19, 19, 4, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 81, 81, 81, 81, 81, 1, 1, 31, 31, 31, 31, 31, 31, 31, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 81, 1, 2, 2, 2] 201 rigid atoms, others: [48, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 250 number of broken/clashed sets: 7 ./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: REAL300024450797 none CC(C)[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 95, 201, 95, 95, 81, 81, 81, 81, 81, 77, 28, 77, 12, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 81, 81, 81, 81, 81, 81, 81, 28, 28, 1, 81, 81, 81, 81] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 609 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450797 none CC(C)[C@@H]1C[C@H]1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 19, 34, 34, 86, 133, 201, 201, 201, 201, 201, 19, 19, 4, 4, 4, 4, 4, 4, 4, 1, 1, 11, 19, 19, 19, 19, 19, 19, 19, 86, 86, 201, 19, 19, 19, 19] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 567 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450797 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450797 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450797/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450797 Building REAL300024450798 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450798' /scratch/stefan/7786230/working/building/REAL300024450798 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450798 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450798/0 /scratch/stefan/7786230/working/building/REAL300024450798 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/691 `/scratch/stefan/7786230/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450798/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450798 none CC1C(NC(=O)C2=CN=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 56, 113, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 7, 1, 1, 15, 15, 15, 15, 15, 15, 56, 56, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 443 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: REAL300024450798 none CC1C(NC(=O)C2=CN=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [155, 155, 155, 155, 181, 181, 181, 201, 201, 201, 201, 201, 155, 155, 155, 152, 65, 152, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 181, 201, 201, 155, 155, 155, 155, 155, 155, 65, 65, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 602 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450798 none CC1C(NC(=O)C2=CN=C(Cl)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 16, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 15, 15, 15, 15, 14, 1, 1, 1, 1, 1, 3, 3, 12, 41, 155, 155, 155, 155, 155, 2, 2, 2, 1, 1, 6, 15, 15, 1, 1, 1, 1, 1, 1, 12, 12, 155] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 263 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450798 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450798 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450798/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450798 Building REAL300024450799 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450799' /scratch/stefan/7786230/working/building/REAL300024450799 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450799 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450799/0 /scratch/stefan/7786230/working/building/REAL300024450799 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/692 `/scratch/stefan/7786230/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC3CCCC23)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450799/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450799 none CC1C(NC(=O)C2=CC3CCCC23)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 25, 25, 61, 80, 128, 128, 128, 128, 128, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 61, 61, 128] 128 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 358 number of broken/clashed sets: 22 ./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: REAL300024450799 none CC1C(NC(=O)C2=CC3CCCC23)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 83, 83, 83, 128, 128, 128, 128, 128, 128, 61, 61, 61, 58, 37, 58, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 83, 128, 128, 128, 128, 128, 128, 128, 128, 128, 61, 61, 61, 61, 61, 61, 37, 37, 1] 128 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 364 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450799 none CC1C(NC(=O)C2=CC3CCCC23)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 13, 23, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 13, 13, 61] 128 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450799 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450799 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450799/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450799 Building REAL300024450800 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450800' /scratch/stefan/7786230/working/building/REAL300024450800 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450800 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450800/0 /scratch/stefan/7786230/working/building/REAL300024450800 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/693 `/scratch/stefan/7786230/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450800/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450800 none CCN1N=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 30, 106, 106, 106, 106, 106, 1, 1, 20, 20, 20, 20, 20, 8, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 106, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 18 ./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: REAL300024450800 none CCN1N=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 150, 150, 150, 150, 150, 130, 130, 130, 106, 106, 106, 106, 106, 102, 30, 102, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 150, 130, 106, 106, 106, 106, 106, 106, 106, 30, 30, 1, 106, 106, 106, 106] 201 rigid atoms, others: [43, 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, 44, 45, 46, 47]) total number of confs: 732 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450800 none CCN1N=CN=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 8, 12, 12, 45, 78, 150, 150, 150, 150, 150, 8, 8, 6, 6, 6, 6, 6, 1, 3, 8, 8, 8, 8, 8, 8, 8, 45, 45, 150, 8, 8, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 353 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450800 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450800 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450800/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450800 Building REAL300024450801 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450801' /scratch/stefan/7786230/working/building/REAL300024450801 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450801 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450801/0 /scratch/stefan/7786230/working/building/REAL300024450801 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/694 `/scratch/stefan/7786230/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450801/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450801 none CC(C)C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 35, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 67, 67, 67, 67, 67, 1, 1, 26, 35, 35, 35, 35, 35, 35, 35, 26, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 67, 1, 2, 2, 2, 26, 26] 201 rigid atoms, others: [45, 43, 49, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52, 53, 54]) total number of confs: 230 number of broken/clashed sets: 44 ./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: REAL300024450801 none CC(C)C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 91, 91, 91, 67, 67, 67, 67, 67, 62, 35, 62, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 67, 67, 67, 67, 67, 67, 67, 35, 35, 1, 67, 67, 67, 67, 201, 201] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 630 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450801 none CC(C)C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 10, 10, 10, 26, 26, 26, 26, 26, 36, 36, 79, 119, 201, 201, 201, 201, 201, 26, 26, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 10, 26, 26, 26, 26, 26, 26, 26, 79, 79, 201, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 53, 54, 36, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 522 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450801 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450801 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450801/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450801 Building REAL300024450802 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450802' /scratch/stefan/7786230/working/building/REAL300024450802 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450802 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450802/0 /scratch/stefan/7786230/working/building/REAL300024450802 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/695 `/scratch/stefan/7786230/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCOC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450802/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450802 none CC1CCOC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 30, 127, 127, 127, 127, 127, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 127, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 253 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: REAL300024450802 none CC1CCOC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 144, 144, 144, 127, 127, 127, 127, 127, 116, 32, 116, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 127, 127, 127, 127, 127, 127, 127, 32, 32, 1, 127, 127, 127, 127] 201 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 710 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450802 none CC1CCOC1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 12, 12, 12, 16, 16, 16, 16, 16, 27, 27, 82, 127, 201, 201, 201, 201, 201, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 12, 16, 16, 16, 16, 16, 16, 16, 82, 82, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 536 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450802 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450802 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450802/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450802 Building REAL300024450803 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450803' /scratch/stefan/7786230/working/building/REAL300024450803 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450803 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450803/0 /scratch/stefan/7786230/working/building/REAL300024450803 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/696 `/scratch/stefan/7786230/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2C[C@H](N=[N+]=[N-])C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450803/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450803 none CC1C(NC(=O)[C@H]2C[C@H](N=[N+]=[N-])C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 1, 12, 12, 12, 12, 12, 20, 20, 49, 73, 157, 157, 157, 157, 157, 12, 12, 12, 12, 12, 10, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 49, 49, 157] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 14, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 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]) total number of confs: 358 number of broken/clashed sets: 18 ./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: REAL300024450803 none CC1C(NC(=O)[C@H]2C[C@H](N=[N+]=[N-])C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 73, 78, 78, 78, 157, 157, 157, 157, 157, 201, 201, 157, 73, 73, 73, 73, 37, 73, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 78, 157, 157, 157, 157, 73, 73, 73, 73, 73, 73, 37, 37, 1] 201 rigid atoms, others: [47, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450803 none CC1C(NC(=O)[C@H]2C[C@H](N=[N+]=[N-])C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 12, 12, 12, 12, 37, 37, 12, 1, 1, 1, 1, 1, 3, 3, 8, 14, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 8, 73] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 40, 41, 42, 39, 44, 15, 16, 17, 18, 19, 43] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450803 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450803 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450803/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450803 Building REAL300024450804 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450804' /scratch/stefan/7786230/working/building/REAL300024450804 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450804 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450804/0 /scratch/stefan/7786230/working/building/REAL300024450804 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/697 `/scratch/stefan/7786230/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CCC(CO2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450804/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450804 none CC1C(NC(=O)C23CCC(CO2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 22, 22, 65, 121, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 65, 65, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 485 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: REAL300024450804 none CC1C(NC(=O)C23CCC(CO2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 104, 104, 119, 119, 119, 201, 201, 201, 201, 201, 201, 104, 104, 104, 101, 46, 101, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 104, 46, 46, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 511 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450804 none CC1C(NC(=O)C23CCC(CO2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 11, 31, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 11, 11, 104] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450804 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450804 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450804/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450804 Building REAL300024450805 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450805' /scratch/stefan/7786230/working/building/REAL300024450805 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450805 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450805/0 /scratch/stefan/7786230/working/building/REAL300024450805 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/698 `/scratch/stefan/7786230/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C3CCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450805/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450805 none CC1C(NC(=O)C2C3CCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 22, 22, 55, 98, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 55, 55, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 437 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: REAL300024450805 none CC1C(NC(=O)C2C3CCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 71, 71, 71, 201, 201, 201, 201, 69, 69, 69, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 71, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 69, 36, 36, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 594 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450805 none CC1C(NC(=O)C2C3CCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 11, 23, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 3, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 11, 11, 69] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450805 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450805 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450805/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450805 Building REAL300024450806 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450806' /scratch/stefan/7786230/working/building/REAL300024450806 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450806 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450806/0 /scratch/stefan/7786230/working/building/REAL300024450806 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/699 `/scratch/stefan/7786230/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450806/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450806 none C=C1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 27, 92, 92, 92, 92, 92, 1, 1, 16, 16, 16, 16, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 92, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 192 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: REAL300024450806 none C=C1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 102, 102, 102, 92, 92, 92, 92, 92, 87, 44, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 201, 201, 201, 102, 92, 92, 92, 92, 92, 92, 92, 44, 44, 1, 92, 92, 92, 92] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 635 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450806 none C=C1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 16, 16, 16, 16, 16, 24, 24, 67, 110, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 16, 16, 16, 67, 67, 201, 16, 16, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 474 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450806 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450806 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450806/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450806 Building REAL300024450807 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450807' /scratch/stefan/7786230/working/building/REAL300024450807 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450807 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450807/0 /scratch/stefan/7786230/working/building/REAL300024450807 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/700 `/scratch/stefan/7786230/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)[C@H]1C) `REAL300024450807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450807/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450807 none C[C@H]1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 36, 99, 99, 99, 99, 99, 1, 1, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 99, 1, 2, 2, 2, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 20 ./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: REAL300024450807 none C[C@H]1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 142, 142, 142, 99, 99, 99, 99, 99, 97, 45, 97, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 142, 99, 99, 99, 99, 99, 99, 99, 45, 45, 1, 99, 99, 99, 99, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 692 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450807 none C[C@H]1C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 17, 17, 51, 93, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 2, 2, 2, 1, 4, 10, 10, 10, 10, 10, 10, 10, 51, 51, 201, 10, 10, 10, 10, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 452 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450807 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450807 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450807/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450807 Building REAL300024450808 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450808' /scratch/stefan/7786230/working/building/REAL300024450808 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450808 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450808/0 /scratch/stefan/7786230/working/building/REAL300024450808 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/701 `/scratch/stefan/7786230/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450808/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450808 none C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [53, 44, 53, 44, 44, 33, 33, 33, 33, 33, 33, 24, 33, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 53, 55, 55, 55, 53, 53, 53, 44, 33, 33, 33, 33, 33, 33, 33, 24, 24, 1, 33, 33, 33, 33, 55, 55, 55, 55, 55, 55] 55 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 208 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450808 none C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 33, 33, 33, 33, 33, 1, 1, 16, 19, 19, 19, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19] 55 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450808 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450808/1 /scratch/stefan/7786230/working/building/REAL300024450808 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/702 `/scratch/stefan/7786230/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C) `REAL300024450808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450808/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450808 none C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 126, 150, 126, 126, 68, 68, 68, 68, 68, 67, 47, 67, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 150, 150, 150, 150, 150, 150, 126, 68, 68, 68, 68, 68, 68, 68, 47, 47, 1, 68, 68, 68, 68, 150, 150, 150, 150, 150, 150] 150 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 514 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450808 none C[C@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 68, 68, 68, 68, 68, 1, 1, 19, 20, 20, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 68, 1, 2, 2, 2, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450808 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450808 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450808/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450808/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450808 Building REAL300024450809 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450809' /scratch/stefan/7786230/working/building/REAL300024450809 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450809 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450809/0 /scratch/stefan/7786230/working/building/REAL300024450809 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/703 `/scratch/stefan/7786230/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(O)C2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450809/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450809 none CC1C(NC(=O)C(O)C2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 40, 31, 31, 11, 31, 1, 11, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 56, 56, 99, 135, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 31, 11, 33, 1, 1, 1, 40, 40, 40, 40, 40, 40, 99, 99, 201] 603 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 601 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: REAL300024450809 none CC1C(NC(=O)C(O)C2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 119, 119, 119, 191, 191, 201, 201, 201, 201, 91, 91, 91, 88, 30, 88, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 119, 191, 573, 201, 201, 201, 91, 91, 91, 91, 91, 91, 30, 30, 1] 603 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1323 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450809 none CC1C(NC(=O)C(O)C2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 15, 15, 40, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 11, 21, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 4, 15, 45, 40, 40, 40, 1, 1, 1, 1, 1, 1, 11, 11, 91] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 275 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450809 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450809 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450809/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450809 Building REAL300024450810 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450810' /scratch/stefan/7786230/working/building/REAL300024450810 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450810 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450810/0 /scratch/stefan/7786230/working/building/REAL300024450810 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/704 `/scratch/stefan/7786230/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450810/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450810 none CCC(C)(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 118, 201, 201, 111, 118, 111, 111, 86, 86, 86, 86, 86, 80, 27, 80, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 354, 111, 86, 86, 86, 86, 86, 86, 86, 27, 27, 1, 86, 86, 86, 86] 603 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 1156 number of broken/clashed sets: 32 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450810 none CCC(C)(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 11, 4, 11, 11, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 86, 86, 86, 86, 86, 1, 1, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 4, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 1, 2, 2, 2] 603 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 234 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450810 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450810 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450810/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450810 Building REAL300024450811 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450811' /scratch/stefan/7786230/working/building/REAL300024450811 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450811 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450811/0 /scratch/stefan/7786230/working/building/REAL300024450811 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/705 `/scratch/stefan/7786230/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450811/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450811 none CC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [175, 175, 173, 173, 115, 115, 115, 85, 85, 85, 85, 85, 80, 41, 80, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 175, 175, 175, 175, 175, 173, 173, 115, 85, 85, 85, 85, 85, 85, 85, 41, 41, 1, 85, 85, 85, 85] 175 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 604 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450811 none CC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 85, 85, 85, 85, 85, 1, 1, 31, 31, 31, 31, 31, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 85, 1, 2, 2, 2] 175 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 228 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450811 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450811 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450811/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450811 Building REAL300024450812 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450812' /scratch/stefan/7786230/working/building/REAL300024450812 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450812 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450812/0 /scratch/stefan/7786230/working/building/REAL300024450812 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/706 `/scratch/stefan/7786230/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450812/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450812 none CC1C(NC(=O)C2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 49, 115, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 4, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 49, 49, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 430 number of broken/clashed sets: 25 ./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: REAL300024450812 none CC1C(NC(=O)C2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 156, 156, 156, 194, 194, 194, 201, 201, 201, 201, 201, 156, 156, 156, 151, 63, 151, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 194, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 63, 63, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 626 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450812 none CC1C(NC(=O)C2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 4, 4, 15, 54, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 4, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 15, 15, 156] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 260 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450812 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450812 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450812/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450812 Building REAL300024450813 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450813' /scratch/stefan/7786230/working/building/REAL300024450813 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450813 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450813/0 /scratch/stefan/7786230/working/building/REAL300024450813 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/707 `/scratch/stefan/7786230/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CC[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450813/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450813 none CC1C(NC(=O)[C@@H]2CC[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 69, 114, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 9, 1, 1, 1, 1, 6, 1, 1, 12, 12, 12, 12, 12, 12, 69, 69, 201] 603 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 36, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 495 number of broken/clashed sets: 123 ./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: REAL300024450813 none CC1C(NC(=O)[C@@H]2CC[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [86, 86, 86, 86, 98, 98, 98, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 84, 41, 84, 12, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 98, 201, 201, 201, 201, 603, 201, 201, 86, 86, 86, 86, 86, 86, 41, 41, 1] 603 rigid atoms, others: [49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 1237 number of broken/clashed sets: 123 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450813 none CC1C(NC(=O)[C@@H]2CC[C@@H](O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 24, 86, 86, 86, 86, 86, 2, 2, 2, 1, 1, 3, 12, 12, 12, 12, 36, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 86] 603 rigid atoms, others: [0, 1, 2, 3, 32, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 46, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450813 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450813 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450813/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450813 Building REAL300024450814 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450814' /scratch/stefan/7786230/working/building/REAL300024450814 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450814 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450814/0 /scratch/stefan/7786230/working/building/REAL300024450814 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/708 `/scratch/stefan/7786230/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450814/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450814 none CC1C(NC(=O)C=CS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 5, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 111, 111, 111, 137, 137, 166, 166, 79, 79, 79, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 111, 137, 137, 166, 166, 166, 79, 79, 79, 79, 79, 79, 39, 39, 1] 166 rigid atoms, others: [44, 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, 43]) total number of confs: 568 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450814 none CC1C(NC(=O)C=CS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 5, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 15, 15, 38, 38, 1, 1, 1, 1, 1, 3, 3, 14, 26, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 5, 15, 15, 38, 38, 38, 1, 1, 1, 1, 1, 1, 14, 14, 79] 166 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450814 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450814 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450814/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450814 Building REAL300024450815 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450815' /scratch/stefan/7786230/working/building/REAL300024450815 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450815 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450815/0 /scratch/stefan/7786230/working/building/REAL300024450815 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/709 `/scratch/stefan/7786230/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450815/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450815 none CC1C(NC(=O)[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 35, 35, 87, 117, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 87, 87, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 547 number of broken/clashed sets: 42 ./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: REAL300024450815 none CC1C(NC(=O)[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [83, 83, 83, 83, 115, 115, 115, 201, 201, 201, 201, 201, 201, 83, 83, 83, 77, 41, 77, 12, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 115, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 83, 83, 83, 41, 41, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 660 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450815 none CC1C(NC(=O)[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 13, 21, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 13, 13, 83] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450815 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450815 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450815/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450815 Building REAL300024450816 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450816' /scratch/stefan/7786230/working/building/REAL300024450816 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450816 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450816/0 /scratch/stefan/7786230/working/building/REAL300024450816 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/710 `/scratch/stefan/7786230/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450816/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450816 none COCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 127, 127, 78, 78, 78, 71, 71, 71, 71, 71, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 127, 127, 78, 71, 71, 71, 71, 71, 71, 71, 29, 29, 1, 71, 71, 71, 71] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 781 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450816 none COCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 24, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 71, 71, 71, 71, 71, 1, 1, 34, 34, 34, 24, 24, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450816 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450816 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450816/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450816 Building REAL300024450817 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450817' /scratch/stefan/7786230/working/building/REAL300024450817 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450817 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450817/0 /scratch/stefan/7786230/working/building/REAL300024450817 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/711 `/scratch/stefan/7786230/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCOC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450817/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450817 none CC1C(NC(=O)CCOC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 39, 39, 17, 39, 9, 5, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 46, 46, 76, 120, 201, 201, 201, 201, 201, 43, 43, 43, 43, 43, 39, 17, 17, 9, 9, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 76, 76, 201] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 534 number of broken/clashed sets: 8 ./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: REAL300024450817 none CC1C(NC(=O)CCOC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 48, 48, 48, 136, 146, 151, 201, 201, 201, 44, 44, 44, 44, 31, 44, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 48, 136, 136, 146, 146, 201, 201, 201, 201, 201, 44, 44, 44, 44, 44, 44, 31, 31, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 786 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450817 none CC1C(NC(=O)CCOC2COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 18, 27, 43, 43, 43, 1, 1, 1, 1, 1, 3, 3, 7, 12, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 3, 13, 13, 18, 18, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 7, 7, 44] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 226 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450817 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450817 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450817/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450817 Building REAL300024450818 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450818' /scratch/stefan/7786230/working/building/REAL300024450818 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450818 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450818/0 /scratch/stefan/7786230/working/building/REAL300024450818 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/712 `/scratch/stefan/7786230/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450818/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450818 none CC(=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 74, 140, 74, 74, 70, 70, 70, 70, 70, 63, 27, 63, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 140, 201, 201, 140, 140, 140, 74, 70, 70, 70, 70, 70, 70, 70, 27, 27, 1, 70, 70, 70, 70, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 674 number of broken/clashed sets: 14 ./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: REAL300024450818 none CC(=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 4, 16, 16, 16, 21, 21, 21, 21, 21, 34, 34, 92, 129, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 4, 4, 4, 16, 21, 21, 21, 21, 21, 21, 21, 92, 92, 201, 21, 21, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 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, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 561 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450818 none CC(=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 70, 70, 70, 70, 70, 1, 1, 11, 21, 21, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 70, 1, 2, 2, 2, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450818 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450818 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450818/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450818 Building REAL300024450819 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450819' /scratch/stefan/7786230/working/building/REAL300024450819 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450819 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450819/0 /scratch/stefan/7786230/working/building/REAL300024450819 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/713 `/scratch/stefan/7786230/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450819/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450819 none CC1C(NC(=O)CCS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 14, 5, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 76, 76, 76, 186, 196, 201, 201, 58, 58, 58, 56, 35, 56, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 76, 186, 186, 196, 196, 201, 201, 201, 58, 58, 58, 58, 58, 58, 35, 35, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 797 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450819 none CC1C(NC(=O)CCS(C)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 14, 5, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 21, 37, 37, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 17, 17, 21, 21, 37, 37, 37, 1, 1, 1, 1, 1, 1, 9, 9, 58] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 233 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450819 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450819 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450819/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450819 Building REAL300024450820 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450820' /scratch/stefan/7786230/working/building/REAL300024450820 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450820 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450820/0 /scratch/stefan/7786230/working/building/REAL300024450820 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/714 `/scratch/stefan/7786230/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN(C)C(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450820/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450820 none CC1C(NC(=O)C2=NN(C)C(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 35, 53, 90, 90, 90, 90, 90, 9, 9, 9, 9, 9, 4, 2, 2, 2, 1, 9, 9, 9, 9, 9, 9, 35, 35, 90] 90 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 228 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: REAL300024450820 none CC1C(NC(=O)C2=NN(C)C(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 85, 85, 85, 90, 90, 90, 90, 90, 90, 71, 71, 71, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 85, 90, 90, 90, 90, 71, 71, 71, 71, 71, 71, 36, 36, 1] 90 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450820 none CC1C(NC(=O)C2=NN(C)C(F)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 8, 5, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 15, 30, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 15, 15, 71] 90 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450820 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450820 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450820/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450820 Building REAL300024450821 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450821' /scratch/stefan/7786230/working/building/REAL300024450821 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450821 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450821/0 /scratch/stefan/7786230/working/building/REAL300024450821 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/715 `/scratch/stefan/7786230/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=C(Cl)Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450821/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450821 none CC1C(NC(=O)C=C(Cl)Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'Cl', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 16, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 106, 106, 106, 127, 127, 127, 201, 201, 201, 106, 106, 106, 104, 54, 104, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 127, 201, 106, 106, 106, 106, 106, 106, 54, 54, 1] 201 rigid atoms, others: [39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 657 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450821 none CC1C(NC(=O)C=C(Cl)Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'Cl', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 16, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 11, 27, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 5, 15, 1, 1, 1, 1, 1, 1, 11, 11, 106] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 10, 11, 12, 13, 14, 34, 35, 27, 28, 31] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450821 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450821 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450821/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450821 Building REAL300024450822 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450822' /scratch/stefan/7786230/working/building/REAL300024450822 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450822 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450822/0 /scratch/stefan/7786230/working/building/REAL300024450822 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/716 `/scratch/stefan/7786230/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C[N-]N=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450822/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450822 none CC1C(NC(=O)C2=C[N-]N=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 64, 118, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 8, 1, 1, 15, 15, 15, 15, 15, 15, 64, 64, 201] 201 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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: 468 number of broken/clashed sets: 10 ./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: REAL300024450822 none CC1C(NC(=O)C2=C[N-]N=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [124, 124, 124, 124, 154, 154, 154, 201, 201, 201, 201, 201, 201, 124, 124, 124, 120, 47, 120, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 154, 201, 201, 124, 124, 124, 124, 124, 124, 47, 47, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 553 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450822 none CC1C(NC(=O)C2=C[N-]N=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 8, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 13, 38, 124, 124, 124, 124, 124, 2, 2, 2, 1, 1, 5, 15, 15, 1, 1, 1, 1, 1, 1, 13, 13, 124] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 35, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450822 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450822 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450822/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450822 Building REAL300024450823 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450823' /scratch/stefan/7786230/working/building/REAL300024450823 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450823 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450823/0 /scratch/stefan/7786230/working/building/REAL300024450823 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/717 `/scratch/stefan/7786230/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450823/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450823 none COC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 35, 35, 35, 35, 35, 1, 1, 6, 7, 7, 7, 6, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 1, 2, 2, 2, 6] 44 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 10 ./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: REAL300024450823 none COC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 37, 37, 37, 35, 35, 35, 35, 35, 35, 26, 35, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 44, 44, 44, 44, 44, 37, 35, 35, 35, 35, 35, 35, 35, 26, 26, 1, 35, 35, 35, 35, 44] 44 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450823 none COC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 8, 8, 17, 24, 44, 44, 44, 44, 44, 6, 6, 1, 2, 2, 2, 1, 4, 6, 6, 6, 6, 6, 6, 6, 17, 17, 44, 6, 6, 6, 6, 1] 44 rigid atoms, others: [1, 2, 3, 4, 5, 6, 46, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450823 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450823 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450823/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450823 Building REAL300024450824 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450824' /scratch/stefan/7786230/working/building/REAL300024450824 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450824 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450824/0 /scratch/stefan/7786230/working/building/REAL300024450824 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/718 `/scratch/stefan/7786230/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450824/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450824 none CC1CN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 87, 87, 87, 87, 87, 1, 1, 28, 28, 28, 28, 28, 28, 28, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 1, 2, 2, 2, 28, 28] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 215 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: REAL300024450824 none CC1CN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 176, 103, 103, 103, 87, 87, 87, 87, 87, 81, 29, 81, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 176, 176, 103, 87, 87, 87, 87, 87, 87, 87, 29, 29, 1, 87, 87, 87, 87, 201, 201] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 709 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450824 none CC1CN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 22, 22, 22, 28, 28, 28, 28, 28, 44, 44, 82, 124, 201, 201, 201, 201, 201, 28, 28, 1, 2, 2, 2, 1, 1, 1, 5, 5, 22, 28, 28, 28, 28, 28, 28, 28, 82, 82, 201, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 49, 50, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 548 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450824 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450824/1 /scratch/stefan/7786230/working/building/REAL300024450824 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/719 `/scratch/stefan/7786230/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[NH+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450824.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450824/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450824 none CC1C[NH+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 9, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 24, 24, 24, 24, 24, 1, 1, 14, 14, 14, 14, 14, 14, 14, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 1, 2, 2, 2, 14, 14] 45 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 27 ./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: REAL300024450824 none CC1C[NH+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 37, 45, 26, 26, 26, 24, 24, 24, 24, 24, 24, 18, 24, 11, 1, 1, 1, 1, 1, 1, 1, 24, 24, 45, 45, 45, 45, 45, 45, 45, 37, 37, 26, 24, 24, 24, 24, 24, 24, 24, 18, 18, 1, 24, 24, 24, 24, 45, 45] 45 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450824 none CC1C[NH+](CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 28, 32, 45, 45, 45, 45, 45, 14, 14, 1, 2, 2, 2, 1, 1, 1, 4, 4, 11, 14, 14, 14, 14, 14, 14, 14, 28, 28, 45, 14, 14, 14, 14, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 50, 51, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450824 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450824 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450824/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450824/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450824 Building REAL300024450825 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450825' /scratch/stefan/7786230/working/building/REAL300024450825 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450825 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450825/0 /scratch/stefan/7786230/working/building/REAL300024450825 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/720 `/scratch/stefan/7786230/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450825/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450825 none CC1C(NC(=O)C(O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 20, 20, 5, 20, 1, 5, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 38, 38, 76, 121, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 20, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 76, 76, 201] 603 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 515 number of broken/clashed sets: 103 ./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: REAL300024450825 none CC1C(NC(=O)C(O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 125, 125, 125, 199, 199, 201, 201, 201, 201, 99, 99, 99, 93, 30, 93, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 125, 199, 597, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 99, 99, 99, 30, 30, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1323 number of broken/clashed sets: 103 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450825 none CC1C(NC(=O)C(O)C2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 20, 20, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 11, 25, 99, 99, 99, 99, 99, 2, 2, 2, 1, 1, 6, 20, 60, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 11, 11, 99] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 317 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450825 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450825 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450825/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450825 Building REAL300024450826 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450826' /scratch/stefan/7786230/working/building/REAL300024450826 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450826 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450826/0 /scratch/stefan/7786230/working/building/REAL300024450826 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/721 `/scratch/stefan/7786230/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450826/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450826 none CC1C(NC(=O)C2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 17, 17, 47, 90, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 7, 2, 2, 2, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 47, 47, 201] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 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: REAL300024450826 none CC1C(NC(=O)C2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 67, 67, 67, 201, 201, 201, 201, 64, 64, 64, 62, 36, 62, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 67, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 64, 64, 64, 36, 36, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 583 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450826 none CC1C(NC(=O)C2(C)COC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 11, 25, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 64] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450826 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450826 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450826/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450826 Building REAL300024450827 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450827' /scratch/stefan/7786230/working/building/REAL300024450827 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450827 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450827/0 /scratch/stefan/7786230/working/building/REAL300024450827 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/722 `/scratch/stefan/7786230/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450827/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450827 none CC1C(NC(=O)C2=CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 18, 18, 43, 60, 102, 102, 102, 102, 102, 13, 13, 13, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 43, 43, 102] 102 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 260 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: REAL300024450827 none CC1C(NC(=O)C2=CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 99, 99, 99, 102, 102, 102, 102, 102, 71, 71, 71, 68, 39, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 99, 102, 102, 102, 102, 102, 102, 102, 71, 71, 71, 71, 71, 71, 39, 39, 1] 102 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 336 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450827 none CC1C(NC(=O)C2=CCCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 16, 29, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 16, 16, 71] 102 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450827 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450827 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450827/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450827 Building REAL300024450828 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450828' /scratch/stefan/7786230/working/building/REAL300024450828 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450828 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450828/0 /scratch/stefan/7786230/working/building/REAL300024450828 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/723 `/scratch/stefan/7786230/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450828/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450828 none CC1C(NC(=O)C2=CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 56, 113, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 56, 56, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 441 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: REAL300024450828 none CC1C(NC(=O)C2=CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 174, 174, 174, 180, 180, 180, 201, 201, 201, 201, 174, 174, 174, 167, 60, 167, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 180, 201, 201, 201, 201, 201, 174, 174, 174, 174, 174, 174, 60, 60, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 563 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450828 none CC1C(NC(=O)C2=CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 16, 51, 174, 174, 174, 174, 174, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 16, 16, 174] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 287 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450828 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450828 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450828/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450828 Building REAL300024450829 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450829' /scratch/stefan/7786230/working/building/REAL300024450829 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450829 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450829/0 /scratch/stefan/7786230/working/building/REAL300024450829 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/724 `/scratch/stefan/7786230/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450829/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450829 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 18, 44, 44, 44, 44, 44, 1, 1, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 1, 2, 2, 2, 13, 13] 94 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 18 ./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: REAL300024450829 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 46, 46, 46, 44, 44, 44, 44, 44, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 94, 94, 94, 94, 94, 46, 44, 44, 44, 44, 44, 44, 44, 28, 28, 1, 44, 44, 44, 44, 94, 94] 94 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 296 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450829 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 13, 13, 13, 13, 13, 18, 18, 49, 64, 94, 94, 94, 94, 94, 13, 13, 1, 2, 2, 2, 1, 11, 13, 13, 13, 13, 13, 13, 13, 49, 49, 94, 13, 13, 13, 13, 1, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 46, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 268 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450829 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450829 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450829/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450829 Building REAL300024450830 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450830' /scratch/stefan/7786230/working/building/REAL300024450830 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450830 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450830/0 /scratch/stefan/7786230/working/building/REAL300024450830 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/725 `/scratch/stefan/7786230/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450830/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450830 none CC1C(NC(=O)C(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 26, 26, 26, 26, 26, 36, 36, 95, 133, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 10, 6, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 95, 95, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 547 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: REAL300024450830 none CC1C(NC(=O)C(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [126, 126, 126, 126, 172, 172, 172, 192, 192, 192, 201, 201, 126, 126, 126, 112, 42, 112, 13, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 172, 192, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 126, 42, 42, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 635 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450830 none CC1C(NC(=O)C(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 9, 9, 9, 26, 26, 1, 1, 1, 1, 1, 3, 3, 16, 33, 126, 126, 126, 126, 126, 2, 2, 2, 1, 1, 6, 9, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 16, 16, 126] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450830 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450830 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450830/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450830 Building REAL300024450831 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450831' /scratch/stefan/7786230/working/building/REAL300024450831 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450831 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450831/0 /scratch/stefan/7786230/working/building/REAL300024450831 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/726 `/scratch/stefan/7786230/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450831/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450831 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 64, 64, 64, 64, 64, 1, 1, 12, 33, 33, 33, 33, 33, 12, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 64, 1, 2, 2, 2, 12, 12] 145 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 14 ./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: REAL300024450831 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 132, 132, 132, 132, 67, 67, 67, 64, 64, 64, 64, 64, 63, 36, 63, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 132, 145, 145, 145, 145, 145, 132, 67, 64, 64, 64, 64, 64, 64, 64, 36, 36, 1, 64, 64, 64, 64, 132, 132] 145 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 492 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450831 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 12, 12, 12, 19, 19, 42, 60, 132, 132, 132, 132, 132, 12, 12, 1, 8, 8, 8, 8, 8, 1, 10, 12, 12, 12, 12, 12, 12, 12, 42, 42, 132, 12, 12, 12, 12, 1, 1] 145 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 49, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450831 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450831 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450831/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450831 Building REAL300024450832 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450832' /scratch/stefan/7786230/working/building/REAL300024450832 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450832 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450832/0 /scratch/stefan/7786230/working/building/REAL300024450832 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/727 `/scratch/stefan/7786230/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450832/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450832 none CC1C(NC(=O)C2CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 58, 110, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 58, 58, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 474 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: REAL300024450832 none CC1C(NC(=O)C2CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 115, 115, 115, 201, 201, 201, 201, 98, 98, 98, 93, 47, 93, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 115, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 47, 47, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 614 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450832 none CC1C(NC(=O)C2CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 32, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 98] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450832 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450832 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450832/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450832 Building REAL300024450833 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450833' /scratch/stefan/7786230/working/building/REAL300024450833 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450833 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450833/0 /scratch/stefan/7786230/working/building/REAL300024450833 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/728 `/scratch/stefan/7786230/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450833/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450833 none CC1C(NC(=O)C2CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 69, 123, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 69, 69, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 462 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: REAL300024450833 none CC1C(NC(=O)C2CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [175, 175, 175, 175, 190, 190, 190, 201, 201, 201, 175, 175, 175, 167, 63, 167, 13, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 190, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 63, 63, 1] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 606 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450833 none CC1C(NC(=O)C2CCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 14, 14, 14, 1, 1, 1, 1, 1, 4, 4, 17, 50, 175, 175, 175, 175, 175, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 17, 17, 175] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 305 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450833 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450833 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450833/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450833 Building REAL300024450834 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450834' /scratch/stefan/7786230/working/building/REAL300024450834 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450834 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450834/0 /scratch/stefan/7786230/working/building/REAL300024450834 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/729 `/scratch/stefan/7786230/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450834/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450834 none CC1C(NC(=O)CCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 59, 59, 59, 60, 60, 60, 165, 178, 201, 201, 59, 59, 59, 59, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 60, 165, 165, 178, 178, 59, 59, 59, 59, 59, 59, 31, 31, 1] 201 rigid atoms, others: [43, 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: 758 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450834 none CC1C(NC(=O)CCN=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 17, 53, 53, 1, 1, 1, 1, 1, 3, 3, 9, 15, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 3, 11, 11, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 59] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450834 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450834 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450834/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450834 Building REAL300024450835 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450835' /scratch/stefan/7786230/working/building/REAL300024450835 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450835 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450835/0 /scratch/stefan/7786230/working/building/REAL300024450835 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/730 `/scratch/stefan/7786230/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450835/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450835 none C#CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 142, 135, 73, 73, 73, 58, 58, 58, 58, 58, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 135, 135, 73, 58, 58, 58, 58, 58, 58, 58, 29, 29, 1, 58, 58, 58, 58] 201 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 875 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450835 none C#CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 22, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 58, 58, 58, 58, 58, 1, 1, 34, 34, 34, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 58, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450835 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450835 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450835/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450835 Building REAL300024450836 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450836' /scratch/stefan/7786230/working/building/REAL300024450836 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450836 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450836/0 /scratch/stefan/7786230/working/building/REAL300024450836 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/731 `/scratch/stefan/7786230/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450836/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450836 none CC1C(NC(=O)CC2=NN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 30, 30, 5, 30, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 54, 54, 85, 125, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 30, 5, 5, 1, 36, 36, 36, 36, 36, 36, 85, 85, 201] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 537 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: REAL300024450836 none CC1C(NC(=O)CC2=NN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 72, 72, 72, 186, 201, 201, 201, 201, 68, 68, 68, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 72, 186, 186, 201, 68, 68, 68, 68, 68, 68, 26, 26, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 707 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450836 none CC1C(NC(=O)CC2=NN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 9, 18, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 3, 18, 18, 36, 1, 1, 1, 1, 1, 1, 9, 9, 68] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450836 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450836 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450836/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450836 Building REAL300024450837 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450837' /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450837 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450837/0 /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/732 `/scratch/stefan/7786230/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN(C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450837/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)CN(C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [86, 86, 86, 86, 108, 108, 108, 191, 191, 191, 201, 201, 86, 86, 86, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 108, 191, 191, 191, 191, 191, 201, 201, 201, 201, 603, 86, 86, 86, 86, 86, 86, 29, 29, 1] 603 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1363 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)CN(C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 15, 15, 20, 26, 1, 1, 1, 1, 1, 3, 3, 11, 20, 86, 86, 86, 86, 86, 2, 2, 2, 1, 1, 3, 12, 12, 15, 15, 15, 20, 20, 26, 26, 78, 1, 1, 1, 1, 1, 1, 11, 11, 86] 603 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 334 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450837/1 /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/733 `/scratch/stefan/7786230/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450837.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450837/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)C[N@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 13, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66, 16, 16, 16, 16, 16, 16, 13, 13, 1] 66 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 46 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)C[N@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 6, 6, 1, 1, 1, 1, 1, 2, 2, 4, 6, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 4, 4, 16] 66 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 80 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450837/2 /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/734 `/scratch/stefan/7786230/working/3D/734' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[N@@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450837.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450837/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)C[N@@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 119, 119, 119, 193, 201, 201, 201, 201, 201, 84, 84, 84, 76, 29, 76, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 119, 193, 193, 201, 201, 201, 201, 201, 201, 201, 603, 84, 84, 84, 84, 84, 84, 29, 29, 1] 603 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1376 number of broken/clashed sets: 241 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450837 none CC1C(NC(=O)C[N@@H+](C)CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 19, 31, 31, 31, 41, 44, 1, 1, 1, 1, 1, 3, 3, 12, 21, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 5, 19, 19, 31, 31, 31, 41, 41, 44, 44, 132, 1, 1, 1, 1, 1, 1, 12, 12, 84] 603 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 484 number of broken/clashed sets: 241 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450837 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450837 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450837/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450837/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450837/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450837 Building REAL300024450838 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450838' /scratch/stefan/7786230/working/building/REAL300024450838 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450838 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450838/0 /scratch/stefan/7786230/working/building/REAL300024450838 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/735 `/scratch/stefan/7786230/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450838/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450838 none CC1C(NC(=O)C2CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 11, 11, 1, 11, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 65, 122, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 11, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 65, 65, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 483 number of broken/clashed sets: 14 ./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: REAL300024450838 none CC1C(NC(=O)C2CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [124, 124, 124, 124, 127, 127, 127, 201, 201, 201, 201, 124, 124, 124, 122, 53, 122, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 127, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 124, 53, 53, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 626 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450838 none CC1C(NC(=O)C2CCCS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 12, 33, 124, 124, 124, 124, 124, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 12, 124] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450838 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450838 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450838/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450838 Building REAL300024450839 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450839' /scratch/stefan/7786230/working/building/REAL300024450839 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450839 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450839/0 /scratch/stefan/7786230/working/building/REAL300024450839 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/736 `/scratch/stefan/7786230/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450839/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450839 none CC1C(NC(=O)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 156, 156, 156, 151, 59, 151, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 603, 156, 156, 156, 156, 156, 156, 59, 59, 1] 603 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 1249 number of broken/clashed sets: 60 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450839 none CC1C(NC(=O)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 11, 35, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 15, 15, 45, 1, 1, 1, 1, 1, 1, 11, 11, 156] 603 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 27, 28, 42] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 325 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450839 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450839 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450839/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450839 Building REAL300024450840 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450840' /scratch/stefan/7786230/working/building/REAL300024450840 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450840 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450840/0 /scratch/stefan/7786230/working/building/REAL300024450840 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/737 `/scratch/stefan/7786230/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450840/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450840 none CC1C(NC(=O)CC2=CC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 24, 24, 6, 24, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 42, 42, 79, 125, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 24, 6, 6, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 79, 79, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 38] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 542 number of broken/clashed sets: 6 ./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: REAL300024450840 none CC1C(NC(=O)CC2=CC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 61, 61, 61, 75, 75, 75, 165, 201, 201, 201, 201, 201, 61, 61, 61, 57, 25, 57, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 75, 165, 165, 201, 201, 201, 201, 61, 61, 61, 61, 61, 61, 25, 25, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 671 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450840 none CC1C(NC(=O)CC2=CC=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 12, 20, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 4, 17, 17, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 12, 12, 61] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450840 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450840 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450840/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450840 Building REAL300024450841 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450841' /scratch/stefan/7786230/working/building/REAL300024450841 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450841 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450841/0 /scratch/stefan/7786230/working/building/REAL300024450841 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/738 `/scratch/stefan/7786230/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CN=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450841/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450841 none CC1C(NC(=O)C2=CC=CN=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 22, 22, 53, 70, 106, 106, 106, 106, 106, 16, 16, 16, 16, 16, 12, 1, 1, 1, 16, 16, 16, 16, 16, 16, 53, 53, 106] 106 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 18 ./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: REAL300024450841 none CC1C(NC(=O)C2=CC=CN=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 60, 60, 60, 106, 106, 106, 106, 106, 106, 58, 58, 58, 55, 35, 55, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 60, 106, 106, 106, 58, 58, 58, 58, 58, 58, 35, 35, 1] 106 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 267 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450841 none CC1C(NC(=O)C2=CC=CN=C2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 8, 1, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 13, 21, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 16, 16, 16, 1, 1, 1, 1, 1, 1, 13, 13, 58] 106 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450841 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450841 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450841/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450841 Building REAL300024450842 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450842' /scratch/stefan/7786230/working/building/REAL300024450842 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450842 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450842/0 /scratch/stefan/7786230/working/building/REAL300024450842 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/739 `/scratch/stefan/7786230/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450842/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450842 none CC1=CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 68, 68, 68, 68, 68, 1, 1, 19, 19, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 68, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 164 number of broken/clashed sets: 24 ./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: REAL300024450842 none CC1=CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 82, 82, 82, 68, 68, 68, 68, 68, 68, 34, 68, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 82, 68, 68, 68, 68, 68, 68, 68, 34, 34, 1, 68, 68, 68, 68] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 613 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450842 none CC1=CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C 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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 19, 19, 19, 19, 19, 28, 28, 61, 116, 201, 201, 201, 201, 201, 19, 19, 2, 2, 2, 1, 1, 13, 19, 19, 19, 19, 19, 19, 19, 61, 61, 201, 19, 19, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 483 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450842 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450842 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450842/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450842 Building REAL300024450843 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450843' /scratch/stefan/7786230/working/building/REAL300024450843 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450843 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450843/0 /scratch/stefan/7786230/working/building/REAL300024450843 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/740 `/scratch/stefan/7786230/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450843/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450843 none CC1C(NC(=O)C(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 56, 56, 56, 96, 96, 96, 141, 137, 137, 141, 56, 56, 56, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 96, 141, 141, 141, 141, 141, 141, 56, 56, 56, 56, 56, 56, 41, 41, 1] 141 rigid atoms, others: [45, 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, 43, 44]) total number of confs: 505 number of broken/clashed sets: 53 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450843 none CC1C(NC(=O)C(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 19, 17, 17, 19, 1, 1, 1, 1, 1, 3, 3, 9, 18, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 6, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 9, 9, 56] 141 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450843 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450843 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450843/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450843 Building REAL300024450844 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450844' /scratch/stefan/7786230/working/building/REAL300024450844 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450844 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450844/0 /scratch/stefan/7786230/working/building/REAL300024450844 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/741 `/scratch/stefan/7786230/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450844/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450844 none CSC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 187, 187, 109, 109, 109, 102, 102, 102, 102, 102, 88, 28, 88, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 187, 187, 109, 102, 102, 102, 102, 102, 102, 102, 28, 28, 1, 102, 102, 102, 102] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 600 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450844 none CSC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 25, 102, 102, 102, 102, 102, 1, 1, 34, 34, 34, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 102, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450844 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450844 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450844/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450844 Building REAL300024450845 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450845' /scratch/stefan/7786230/working/building/REAL300024450845 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450845 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450845/0 /scratch/stefan/7786230/working/building/REAL300024450845 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/742 `/scratch/stefan/7786230/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CNC=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450845/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450845 none CC1C(NC(=O)C2=CNC=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 49, 71, 112, 112, 112, 112, 112, 11, 11, 11, 11, 11, 8, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 49, 49, 112] 112 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 287 number of broken/clashed sets: 24 ./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: REAL300024450845 none CC1C(NC(=O)C2=CNC=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 97, 97, 97, 112, 112, 112, 112, 112, 112, 83, 83, 83, 72, 34, 72, 12, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 97, 112, 112, 112, 112, 83, 83, 83, 83, 83, 83, 34, 34, 1] 112 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 337 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450845 none CC1C(NC(=O)C2=CNC=CC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 8, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 16, 34, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 4, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 16, 16, 83] 112 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450845 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450845 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450845/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450845 Building REAL300024450846 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450846' /scratch/stefan/7786230/working/building/REAL300024450846 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450846 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450846/0 /scratch/stefan/7786230/working/building/REAL300024450846 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/743 `/scratch/stefan/7786230/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CS1) `REAL300024450846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450846/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450846 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 26, 78, 78, 78, 78, 78, 1, 1, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 78, 1, 2, 2, 2, 12, 12] 136 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 23 ./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: REAL300024450846 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 89, 89, 89, 78, 78, 78, 78, 78, 75, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 136, 136, 136, 136, 136, 136, 89, 78, 78, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 78, 78, 136, 136] 136 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 439 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450846 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 12, 12, 12, 19, 19, 61, 86, 136, 136, 136, 136, 136, 12, 12, 1, 1, 2, 2, 2, 1, 10, 12, 12, 12, 12, 12, 12, 12, 61, 61, 136, 12, 12, 12, 12, 1, 1] 136 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450846 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450846 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450846/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450846 Building REAL300024450847 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450847' /scratch/stefan/7786230/working/building/REAL300024450847 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450847 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450847/0 /scratch/stefan/7786230/working/building/REAL300024450847 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/744 `/scratch/stefan/7786230/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450847/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450847 none CCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 12, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2] 12 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 25 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450847 none CCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2] 12 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450847 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450847 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450847/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450847 Building REAL300024450848 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450848' /scratch/stefan/7786230/working/building/REAL300024450848 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450848 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450848/0 /scratch/stefan/7786230/working/building/REAL300024450848 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/745 `/scratch/stefan/7786230/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450848/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450848 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 25, 96, 96, 96, 96, 96, 1, 1, 10, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 96, 1, 2, 2, 2] 166 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 258 number of broken/clashed sets: 27 ./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: REAL300024450848 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [166, 135, 135, 135, 135, 126, 126, 126, 96, 96, 96, 96, 96, 89, 40, 89, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 135, 166, 166, 166, 166, 166, 126, 96, 96, 96, 96, 96, 96, 96, 40, 40, 1, 96, 96, 96, 96] 166 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 623 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450848 none CCC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 15, 15, 40, 57, 135, 135, 135, 135, 135, 10, 10, 1, 8, 8, 8, 8, 8, 5, 10, 10, 10, 10, 10, 10, 10, 40, 40, 135, 10, 10, 10, 10] 166 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 323 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450848 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450848 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450848/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450848 Building REAL300024450849 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450849' /scratch/stefan/7786230/working/building/REAL300024450849 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450849 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450849/0 /scratch/stefan/7786230/working/building/REAL300024450849 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/746 `/scratch/stefan/7786230/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C[NH+](C)C) `REAL300024450849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450849/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450849 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 196, 139, 139, 139, 85, 85, 85, 85, 85, 75, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 200, 201, 201, 201, 201, 200, 200, 200, 200, 196, 196, 139, 85, 85, 85, 85, 85, 85, 85, 29, 29, 1, 85, 85, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 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, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 761 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450849 none CC(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 85, 85, 85, 85, 85, 1, 1, 21, 27, 27, 27, 27, 21, 21, 21, 21, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 85, 1, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 39, 45, 11, 40, 21, 22, 41, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450849 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450849 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450849/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450849 Building REAL300024450850 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450850' /scratch/stefan/7786230/working/building/REAL300024450850 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450850 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450850/0 /scratch/stefan/7786230/working/building/REAL300024450850 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/747 `/scratch/stefan/7786230/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1) `REAL300024450850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450850/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450850 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 65, 65, 65, 65, 65, 1, 1, 37, 37, 37, 37, 37, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 8 ./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: REAL300024450850 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 167, 69, 69, 69, 65, 65, 65, 65, 65, 61, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 167, 167, 69, 65, 65, 65, 65, 65, 65, 65, 28, 28, 1, 65, 65, 65, 65] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 679 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450850 none CC1=NN(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 33, 33, 33, 37, 37, 37, 37, 37, 52, 52, 85, 125, 201, 201, 201, 201, 201, 37, 37, 1, 1, 2, 2, 2, 7, 7, 33, 37, 37, 37, 37, 37, 37, 37, 85, 85, 201, 37, 37, 37, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450850 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450850 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450850/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450850 Building REAL300024450851 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450851' /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450851 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450851/0 /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/748 `/scratch/stefan/7786230/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450851/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 25, 25, 25, 21, 21, 21, 21, 21, 21, 17, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 25, 21, 21, 21, 21, 21, 21, 21, 17, 17, 1, 21, 21, 21, 21] 30 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CC[N@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 8, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 21, 21, 21, 21, 21, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 1, 2, 2, 2] 30 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 78 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450851/1 /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/749 `/scratch/stefan/7786230/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450851.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450851/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 187, 201, 201, 121, 121, 121, 80, 80, 80, 80, 80, 73, 28, 73, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 121, 80, 80, 80, 80, 80, 80, 80, 28, 28, 1, 80, 80, 80, 80] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 817 number of broken/clashed sets: 199 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CC[N@@H+](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 20, 35, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 80, 80, 80, 80, 80, 1, 1, 39, 39, 39, 39, 39, 35, 35, 35, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 80, 1, 2, 2, 2] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 311 number of broken/clashed sets: 199 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450851/2 /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/750 `/scratch/stefan/7786230/working/3D/750' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450851.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450851/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CCN(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 200, 201, 126, 126, 126, 89, 89, 89, 89, 89, 84, 27, 84, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 126, 89, 89, 89, 89, 89, 89, 89, 27, 27, 1, 89, 89, 89, 89] 201 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 799 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450851 none CCN(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 22, 16, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 89, 89, 89, 89, 89, 1, 1, 26, 26, 26, 26, 26, 22, 22, 22, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 89, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 249 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450851 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450851 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450851/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450851/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450851/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450851 Building REAL300024450852 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450852' /scratch/stefan/7786230/working/building/REAL300024450852 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450852 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450852/0 /scratch/stefan/7786230/working/building/REAL300024450852 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/751 `/scratch/stefan/7786230/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(C)(C)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450852/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450852 none CC1C(NC(=O)CCC(C)(C)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 70, 70, 70, 157, 157, 201, 201, 201, 62, 62, 62, 60, 37, 60, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 70, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 37, 37, 1] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 897 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450852 none CC1C(NC(=O)CCC(C)(C)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 8, 14, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 8, 8, 62] 201 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450852 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450852 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450852/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450852 Building REAL300024450853 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450853' /scratch/stefan/7786230/working/building/REAL300024450853 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450853 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450853/0 /scratch/stefan/7786230/working/building/REAL300024450853 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/752 `/scratch/stefan/7786230/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024450853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450853/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450853 none CC[C@H](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 165, 189, 58, 58, 58, 45, 45, 45, 45, 45, 42, 22, 42, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 189, 201, 201, 201, 201, 201, 201, 201, 165, 165, 58, 45, 45, 45, 45, 45, 45, 45, 22, 22, 1, 45, 45, 45, 45, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 901 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450853 none CC[C@H](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 27, 16, 28, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 45, 45, 45, 45, 45, 1, 1, 26, 32, 32, 31, 31, 31, 31, 31, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450853 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450853 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450853/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450853 Building REAL300024450854 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450854' /scratch/stefan/7786230/working/building/REAL300024450854 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450854 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450854/0 /scratch/stefan/7786230/working/building/REAL300024450854 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/753 `/scratch/stefan/7786230/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450854/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450854 none CCC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 156, 156, 71, 71, 71, 57, 57, 57, 57, 57, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 159, 159, 156, 156, 71, 57, 57, 57, 57, 57, 57, 57, 31, 31, 1, 57, 57, 57, 57] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 764 number of broken/clashed sets: 43 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450854 none CCC=CC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 17, 17, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 57, 57, 57, 57, 57, 1, 1, 33, 33, 33, 33, 33, 17, 17, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 57, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450854 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450854 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450854/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450854 Building REAL300024450855 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450855' /scratch/stefan/7786230/working/building/REAL300024450855 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450855 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450855/0 /scratch/stefan/7786230/working/building/REAL300024450855 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/754 `/scratch/stefan/7786230/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(=CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450855/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450855 none CC1CCC(=CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 23, 80, 80, 80, 80, 80, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 80, 1, 2, 2, 2, 16, 16] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 38 ./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: REAL300024450855 none CC1CCC(=CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 86, 86, 86, 80, 80, 80, 80, 80, 77, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 80, 80, 80, 80, 80, 80, 80, 38, 38, 1, 80, 80, 80, 80, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 617 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450855 none CC1CCC(=CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 10, 16, 16, 16, 16, 16, 23, 23, 79, 115, 201, 201, 201, 201, 201, 16, 16, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 16, 16, 16, 79, 79, 201, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 51, 34, 35, 52, 26, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 529 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450855 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450855 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450855/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450855 Building REAL300024450856 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450856' /scratch/stefan/7786230/working/building/REAL300024450856 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450856 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450856/0 /scratch/stefan/7786230/working/building/REAL300024450856 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/755 `/scratch/stefan/7786230/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450856/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450856 none CC1C(NC(=O)C2=CC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 9, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 17] 17 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 34 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: REAL300024450856 none CC1C(NC(=O)C2=CC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 17, 11, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 1] 17 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450856 none CC1C(NC(=O)C2=CC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 9, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 17] 17 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450856 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450856 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450856/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450856 Building REAL300024450857 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450857' /scratch/stefan/7786230/working/building/REAL300024450857 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450857 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450857/0 /scratch/stefan/7786230/working/building/REAL300024450857 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/756 `/scratch/stefan/7786230/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1) `REAL300024450857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450857/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450857 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 36, 120, 120, 120, 120, 120, 1, 1, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 120, 1, 2, 2, 2, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 212 number of broken/clashed sets: 29 ./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: REAL300024450857 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 134, 134, 134, 120, 120, 120, 120, 120, 115, 50, 115, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 134, 120, 120, 120, 120, 120, 120, 120, 50, 50, 1, 120, 120, 120, 120, 201, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 537 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450857 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 8, 8, 8, 8, 8, 14, 14, 52, 108, 201, 201, 201, 201, 201, 8, 8, 1, 1, 2, 2, 2, 1, 5, 8, 8, 8, 8, 8, 8, 8, 52, 52, 201, 8, 8, 8, 8, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 446 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450857 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450857 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450857/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450857 Building REAL300024450858 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450858' /scratch/stefan/7786230/working/building/REAL300024450858 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450858 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450858/0 /scratch/stefan/7786230/working/building/REAL300024450858 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/757 `/scratch/stefan/7786230/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450858/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450858 none COCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 198, 100, 198, 198, 100, 100, 77, 77, 77, 77, 77, 74, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 198, 198, 198, 594, 100, 77, 77, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77, 77, 77] 603 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 1368 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450858 none COCC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 22, 13, 4, 13, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 77, 77, 77, 77, 77, 1, 1, 31, 31, 31, 22, 22, 13, 13, 13, 39, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 77, 1, 2, 2, 2] 603 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 276 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450858 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450858 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450858/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450858 Building REAL300024450859 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450859' /scratch/stefan/7786230/working/building/REAL300024450859 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450859 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450859/0 /scratch/stefan/7786230/working/building/REAL300024450859 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/758 `/scratch/stefan/7786230/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450859/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450859 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 67, 67, 67, 67, 67, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 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: REAL300024450859 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 77, 77, 67, 67, 67, 67, 67, 67, 35, 67, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 77, 67, 67, 67, 67, 67, 67, 67, 35, 35, 1, 67, 67, 67, 67, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 433 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450859 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 15, 15, 15, 15, 15, 22, 22, 50, 94, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 15, 15, 15, 15, 50, 50, 201, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 433 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450859 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450859 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450859/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450859 Building REAL300024450860 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450860' /scratch/stefan/7786230/working/building/REAL300024450860 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450860 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450860/0 /scratch/stefan/7786230/working/building/REAL300024450860 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/759 `/scratch/stefan/7786230/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450860/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450860 none C=C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 22, 71, 71, 71, 71, 71, 1, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 71, 1, 2, 2, 2, 23, 23] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 41, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 190 number of broken/clashed sets: 39 ./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: REAL300024450860 none C=C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 91, 91, 91, 71, 71, 71, 71, 71, 66, 41, 66, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 91, 71, 71, 71, 71, 71, 71, 71, 41, 41, 1, 71, 71, 71, 71, 201, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 650 number of broken/clashed sets: 39 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450860 none C=C1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 23, 23, 23, 23, 23, 35, 35, 91, 127, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 91, 91, 201, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450860 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450860 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450860/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450860 Building REAL300024450861 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450861' /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450861 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450861/0 /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/760 `/scratch/stefan/7786230/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450861/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CC[N@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 26, 24, 24, 24, 21, 21, 21, 21, 21, 21, 16, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 21, 21, 21, 21, 21, 21, 21, 16, 16, 1, 21, 21, 21, 21, 26, 26, 26, 26, 26] 26 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 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: REAL300024450861 none CC[N@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 1, 3, 3, 4, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 19, 20, 26, 26, 26, 26, 26, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 9, 12, 12, 12, 12, 12, 12, 12, 19, 19, 26, 12, 12, 12, 12, 1, 1, 1, 1, 1] 26 rigid atoms, others: [2, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 94 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CC[N@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 8, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 21, 21, 21, 21, 21, 1, 1, 9, 12, 12, 9, 9, 9, 9, 9, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 1, 2, 2, 2, 12, 12, 12, 12, 12] 26 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450861/1 /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/761 `/scratch/stefan/7786230/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450861.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450861/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CC[N@@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 36, 37, 30, 30, 30, 29, 29, 29, 29, 29, 29, 20, 29, 13, 1, 1, 1, 1, 1, 1, 1, 29, 29, 37, 37, 37, 37, 37, 37, 37, 37, 36, 36, 30, 29, 29, 29, 29, 29, 29, 29, 20, 20, 1, 29, 29, 29, 29, 37, 37, 37, 37, 37] 37 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 29 ./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: REAL300024450861 none CC[N@@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 3, 6, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 24, 29, 37, 37, 37, 37, 37, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 10, 12, 12, 12, 12, 12, 12, 12, 24, 24, 37, 12, 12, 12, 12, 1, 1, 1, 1, 1] 37 rigid atoms, others: [2, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 143 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CC[N@@H+](CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 6, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 29, 29, 29, 29, 29, 1, 1, 9, 12, 12, 10, 10, 10, 10, 10, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 1, 2, 2, 2, 12, 12, 12, 12, 12] 37 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450861/2 /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/762 `/scratch/stefan/7786230/working/3D/762' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024450861.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450861/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CCN(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 195, 103, 103, 103, 76, 76, 76, 76, 76, 71, 27, 71, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 103, 76, 76, 76, 76, 76, 76, 76, 27, 27, 1, 76, 76, 76, 76, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 755 number of broken/clashed sets: 14 ./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: REAL300024450861 none CCN(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 3, 9, 20, 20, 20, 26, 26, 26, 26, 26, 40, 40, 81, 123, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 20, 26, 26, 26, 26, 26, 26, 26, 81, 81, 201, 26, 26, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 49, 50, 51, 52, 53, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 555 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450861 none CCN(CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 20, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 76, 76, 76, 76, 76, 1, 1, 20, 26, 26, 24, 24, 24, 24, 24, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 76, 1, 2, 2, 2, 26, 26, 26, 26, 26] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 251 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450861 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450861 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450861/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450861/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450861/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450861 Building REAL300024450862 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450862' /scratch/stefan/7786230/working/building/REAL300024450862 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450862 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450862/0 /scratch/stefan/7786230/working/building/REAL300024450862 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/763 `/scratch/stefan/7786230/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450862/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450862 none CC1C(NC(=O)C(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 495 conformations in input total number of sets (complete confs): 495 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 15, 6, 15, 1, 6, 6, 1, 1, 1, 30, 30, 30, 30, 30, 43, 43, 77, 110, 165, 165, 165, 165, 165, 30, 30, 30, 30, 30, 15, 7, 7, 7, 18, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 77, 77, 165] 495 rigid atoms, others: [36, 37, 6, 39, 40, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 480 number of broken/clashed sets: 156 ./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: REAL300024450862 none CC1C(NC(=O)C(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 495 conformations in input total number of sets (complete confs): 495 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 132, 132, 132, 165, 164, 165, 165, 165, 75, 75, 75, 73, 54, 73, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 132, 165, 165, 165, 495, 165, 165, 165, 165, 165, 75, 75, 75, 75, 75, 75, 54, 54, 1] 495 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1135 number of broken/clashed sets: 156 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450862 none CC1C(NC(=O)C(C)(O)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 495 conformations in input total number of sets (complete confs): 495 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 18, 20, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 21, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 6, 20, 20, 20, 60, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 75] 495 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 292 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450862 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450862 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450862/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450862 Building REAL300024450863 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450863' /scratch/stefan/7786230/working/building/REAL300024450863 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450863 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450863/0 /scratch/stefan/7786230/working/building/REAL300024450863 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/764 `/scratch/stefan/7786230/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024450863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450863/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450863 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 33, 83, 83, 83, 83, 83, 1, 1, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 83, 1, 2, 2, 2] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 22 ./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: REAL300024450863 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 97, 97, 97, 87, 87, 87, 83, 83, 83, 83, 83, 76, 40, 76, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 97, 97, 97, 97, 97, 87, 83, 83, 83, 83, 83, 83, 83, 40, 40, 1, 83, 83, 83, 83] 97 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 305 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450863 none CC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 11, 11, 34, 52, 97, 97, 97, 97, 97, 10, 10, 1, 2, 2, 2, 1, 5, 10, 10, 10, 10, 10, 10, 10, 34, 34, 97, 10, 10, 10, 10] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450863 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450863 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450863/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450863 Building REAL300024450864 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450864' /scratch/stefan/7786230/working/building/REAL300024450864 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450864 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450864/0 /scratch/stefan/7786230/working/building/REAL300024450864 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/765 `/scratch/stefan/7786230/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=C(Cl)C=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450864/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450864 none CC1C(NC(=O)C2=C(Cl)C=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 51, 99, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 6, 1, 1, 14, 14, 14, 14, 14, 14, 51, 51, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 431 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: REAL300024450864 none CC1C(NC(=O)C2=C(Cl)C=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 106, 106, 106, 201, 201, 201, 201, 201, 98, 98, 98, 94, 45, 94, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 106, 201, 201, 98, 98, 98, 98, 98, 98, 45, 45, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 485 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450864 none CC1C(NC(=O)C2=C(Cl)C=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 36, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 6, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 98] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450864 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450864/1 /scratch/stefan/7786230/working/building/REAL300024450864 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/766 `/scratch/stefan/7786230/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NNC=C2Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450864.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450864/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450864 none CC1C(NC(=O)C2=NNC=C2Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 1, 16, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 45, 94, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 7, 1, 1, 9, 9, 9, 9, 9, 9, 45, 45, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 415 number of broken/clashed sets: 20 ./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: REAL300024450864 none CC1C(NC(=O)C2=NNC=C2Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 1, 16, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 92, 100, 100, 100, 201, 201, 201, 201, 201, 92, 92, 92, 89, 45, 89, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 100, 201, 201, 92, 92, 92, 92, 92, 92, 45, 45, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 469 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450864 none CC1C(NC(=O)C2=NNC=C2Cl)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 1, 16, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 12, 33, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 3, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 92] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450864 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450864 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450864/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450864/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450864 Building REAL300024450865 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450865' /scratch/stefan/7786230/working/building/REAL300024450865 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450865 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450865/0 /scratch/stefan/7786230/working/building/REAL300024450865 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/767 `/scratch/stefan/7786230/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CS1) `REAL300024450865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450865/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450865 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 36, 99, 99, 99, 99, 99, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 99, 1, 2, 2, 2, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 18 ./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: REAL300024450865 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 131, 131, 131, 99, 99, 99, 99, 99, 94, 44, 94, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 131, 99, 99, 99, 99, 99, 99, 99, 44, 44, 1, 99, 99, 99, 99, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 555 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450865 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N=CS1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 13, 13, 13, 13, 13, 19, 19, 52, 100, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 13, 52, 52, 201, 13, 13, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 439 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450865 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450865 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450865/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450865 Building REAL300024450866 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450866' /scratch/stefan/7786230/working/building/REAL300024450866 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450866 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450866/0 /scratch/stefan/7786230/working/building/REAL300024450866 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/768 `/scratch/stefan/7786230/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450866/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450866 none CC1C(NC(=O)C2CCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 65, 124, 201, 201, 201, 201, 201, 15, 15, 15, 15, 15, 10, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 65, 65, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 480 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: REAL300024450866 none CC1C(NC(=O)C2CCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 102, 102, 102, 107, 107, 107, 201, 201, 201, 201, 102, 102, 102, 98, 51, 98, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 107, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 102, 51, 51, 1] 201 rigid atoms, others: [45, 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, 43, 44]) total number of confs: 624 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450866 none CC1C(NC(=O)C2CCC2F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 12, 32, 102, 102, 102, 102, 102, 2, 2, 2, 1, 1, 3, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 12, 12, 102] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 203 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450866 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450866 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450866/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450866 Building REAL300024450867 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450867' /scratch/stefan/7786230/working/building/REAL300024450867 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450867 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450867/0 /scratch/stefan/7786230/working/building/REAL300024450867 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/769 `/scratch/stefan/7786230/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450867/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450867 none CC[NH+](CC)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 154, 154, 153, 92, 92, 92, 63, 63, 63, 63, 63, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 63, 63, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 153, 153, 92, 63, 63, 63, 63, 63, 63, 63, 28, 28, 1, 63, 63, 63, 63] 154 rigid atoms, others: [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, 48, 49, 50, 51, 53, 54, 55, 56]) total number of confs: 629 number of broken/clashed sets: 154 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450867 none CC[NH+](CC)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [21, 18, 13, 18, 18, 21, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 63, 63, 63, 63, 63, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 63, 1, 2, 2, 2] 154 rigid atoms, others: [16, 11, 15, 44, 10, 43, 12, 13, 14, 45, 48, 49, 46, 27, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 218 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450867 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450867 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450867/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450867 Building REAL300024450868 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450868' /scratch/stefan/7786230/working/building/REAL300024450868 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450868 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450868/0 /scratch/stefan/7786230/working/building/REAL300024450868 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/770 `/scratch/stefan/7786230/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450868/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450868 none CC1C(NC(=O)C2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 32, 74, 150, 150, 150, 150, 150, 8, 8, 8, 8, 8, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 32, 32, 150] 150 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 306 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: REAL300024450868 none CC1C(NC(=O)C2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 112, 112, 112, 150, 150, 150, 150, 111, 111, 111, 109, 52, 109, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 112, 150, 150, 150, 111, 111, 111, 111, 111, 111, 52, 52, 1] 150 rigid atoms, others: [42, 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]) total number of confs: 423 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450868 none CC1C(NC(=O)C2=CN=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 14, 42, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 3, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 14, 111] 150 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450868 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450868 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450868/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450868 Building REAL300024450869 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450869' /scratch/stefan/7786230/working/building/REAL300024450869 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450869 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450869/0 /scratch/stefan/7786230/working/building/REAL300024450869 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/771 `/scratch/stefan/7786230/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450869/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450869 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 26, 73, 73, 73, 73, 73, 1, 1, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 73, 1, 2, 2, 2] 94 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 164 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: REAL300024450869 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 87, 87, 87, 73, 73, 73, 73, 73, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 94, 94, 94, 94, 87, 73, 73, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 73, 73] 94 rigid atoms, others: [39, 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, 37, 38, 40, 41, 42, 43]) total number of confs: 309 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450869 none CC1=NOC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 19, 19, 41, 54, 94, 94, 94, 94, 94, 12, 12, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 12, 12, 41, 41, 94, 12, 12, 12, 12] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25] set([6, 7, 8, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 249 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450869 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450869 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450869/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450869 Building REAL300024450870 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450870' /scratch/stefan/7786230/working/building/REAL300024450870 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450870 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450870/0 /scratch/stefan/7786230/working/building/REAL300024450870 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/772 `/scratch/stefan/7786230/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450870/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450870 none CC1C(NC(=O)C2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 36, 36, 91, 127, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 91, 91, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 553 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: REAL300024450870 none CC1C(NC(=O)C2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 96, 96, 96, 201, 201, 201, 201, 201, 62, 62, 62, 59, 36, 59, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 36, 36, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 645 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450870 none CC1C(NC(=O)C2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 3, 3, 13, 21, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 13, 13, 62] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450870 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450870 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450870/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450870 Building REAL300024450871 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450871' /scratch/stefan/7786230/working/building/REAL300024450871 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450871 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450871/0 /scratch/stefan/7786230/working/building/REAL300024450871 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/773 `/scratch/stefan/7786230/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450871/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450871 none CC1C(NC(=O)CC2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 33, 33, 85, 119, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 12, 4, 4, 1, 1, 1, 23, 23, 23, 23, 23, 23, 85, 85, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 524 number of broken/clashed sets: 39 ./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: REAL300024450871 none CC1C(NC(=O)CC2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 81, 81, 113, 113, 113, 201, 201, 201, 201, 201, 201, 81, 81, 81, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 113, 201, 201, 201, 201, 201, 81, 81, 81, 81, 81, 81, 39, 39, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 820 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450871 none CC1C(NC(=O)CC2=CN=CN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 13, 19, 19, 16, 19, 19, 1, 1, 1, 1, 1, 3, 3, 14, 25, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 4, 13, 13, 19, 19, 19, 1, 1, 1, 1, 1, 1, 14, 14, 81] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 218 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450871 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450871 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450871/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450871 Building REAL300024450872 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450872' /scratch/stefan/7786230/working/building/REAL300024450872 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450872 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450872/0 /scratch/stefan/7786230/working/building/REAL300024450872 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/774 `/scratch/stefan/7786230/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450872/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450872 none CC1=NSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 27, 77, 77, 77, 77, 77, 1, 1, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 77, 1, 2, 2, 2, 17] 137 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 28 ./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: REAL300024450872 none CC1=NSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 109, 109, 109, 77, 77, 77, 77, 77, 71, 39, 71, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 137, 137, 137, 137, 109, 77, 77, 77, 77, 77, 77, 77, 39, 39, 1, 77, 77, 77, 77, 137] 137 rigid atoms, others: [39, 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, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 422 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450872 none CC1=NSC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 26, 26, 63, 85, 137, 137, 137, 137, 137, 17, 17, 1, 2, 2, 2, 7, 17, 17, 17, 17, 17, 17, 17, 63, 63, 137, 17, 17, 17, 17, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 25] set([6, 7, 8, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450872 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450872 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450872/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450872 Building REAL300024450873 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450873' /scratch/stefan/7786230/working/building/REAL300024450873 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450873 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450873/0 /scratch/stefan/7786230/working/building/REAL300024450873 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/775 `/scratch/stefan/7786230/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450873/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450873 none CC1C(NC(=O)C2=CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 23, 23, 61, 114, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 12, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 61, 61, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 451 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: REAL300024450873 none CC1C(NC(=O)C2=CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [138, 138, 138, 138, 148, 148, 148, 201, 201, 201, 201, 138, 138, 138, 135, 57, 135, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 148, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 57, 57, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 547 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450873 none CC1C(NC(=O)C2=CCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 14, 40, 138, 138, 138, 138, 138, 2, 2, 2, 1, 1, 4, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 14, 14, 138] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 243 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450873 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450873 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450873/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450873 Building REAL300024450874 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450874' /scratch/stefan/7786230/working/building/REAL300024450874 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450874 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450874/0 /scratch/stefan/7786230/working/building/REAL300024450874 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/776 `/scratch/stefan/7786230/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450874/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450874 none CC1C(NC(=O)CCCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 31, 32, 32, 32, 156, 176, 201, 201, 201, 31, 31, 31, 30, 21, 30, 13, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 32, 156, 156, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 31, 21, 21, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 955 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450874 none CC1C(NC(=O)CCCC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 15, 19, 43, 43, 1, 1, 1, 1, 1, 3, 3, 7, 11, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 3, 11, 11, 19, 19, 19, 19, 43, 1, 1, 1, 1, 1, 1, 7, 7, 31] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450874 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450874 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450874/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450874 Building REAL300024450875 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450875' /scratch/stefan/7786230/working/building/REAL300024450875 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450875 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450875/0 /scratch/stefan/7786230/working/building/REAL300024450875 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/777 `/scratch/stefan/7786230/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450875/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450875 none CC1C(NC(=O)CN2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 22, 22, 6, 22, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 44, 44, 85, 127, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 22, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 28, 28, 28, 28, 28, 28, 85, 85, 201] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 44, 43] set([0, 1, 2, 3, 4, 5, 13, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 556 number of broken/clashed sets: 6 ./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: REAL300024450875 none CC1C(NC(=O)CN2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 86, 86, 86, 191, 201, 201, 201, 201, 201, 77, 77, 77, 74, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 86, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 77, 29, 29, 1] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 715 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450875 none CC1C(NC(=O)CN2CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 12, 21, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 3, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 12, 12, 77] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 13, 14, 45, 16, 49, 50, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450875 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450875 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450875/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450875 Building REAL300024450876 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450876' /scratch/stefan/7786230/working/building/REAL300024450876 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450876 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450876/0 /scratch/stefan/7786230/working/building/REAL300024450876 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/778 `/scratch/stefan/7786230/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450876/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450876 none CCCC(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 163, 142, 163, 64, 64, 64, 62, 62, 62, 62, 62, 57, 24, 57, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 163, 489, 142, 142, 64, 62, 62, 62, 62, 62, 62, 62, 24, 24, 1, 62, 62, 62, 62] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1329 number of broken/clashed sets: 36 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450876 none CCCC(O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 23, 12, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 62, 62, 62, 62, 62, 1, 1, 32, 32, 32, 32, 32, 32, 32, 23, 69, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 62, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 325 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450876 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450876 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450876/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450876 Building REAL300024450877 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450877' /scratch/stefan/7786230/working/building/REAL300024450877 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450877 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450877/0 /scratch/stefan/7786230/working/building/REAL300024450877 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/779 `/scratch/stefan/7786230/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450877/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450877 none CC1C(NC(=O)C2(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 9, 9, 1, 9, 1, 1, 1, 1, 16, 16, 16, 16, 16, 26, 26, 71, 122, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 71, 71, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 506 number of broken/clashed sets: 18 ./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: REAL300024450877 none CC1C(NC(=O)C2(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [111, 111, 111, 111, 128, 128, 128, 201, 201, 201, 111, 111, 111, 110, 56, 110, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 128, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111, 56, 56, 1] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 673 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450877 none CC1C(NC(=O)C2(Cl)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 16, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 11, 26, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 11, 11, 111] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 10, 11, 12, 13, 14, 34, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450877 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450877 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450877/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450877 Building REAL300024450878 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450878' /scratch/stefan/7786230/working/building/REAL300024450878 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450878 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450878/0 /scratch/stefan/7786230/working/building/REAL300024450878 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/780 `/scratch/stefan/7786230/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450878/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450878 none CC1C(NC(=O)C2=CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 56, 110, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 56, 56, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 439 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: REAL300024450878 none CC1C(NC(=O)C2=CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [155, 155, 155, 155, 193, 193, 193, 201, 201, 201, 201, 155, 155, 155, 148, 69, 148, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 193, 201, 201, 201, 201, 201, 155, 155, 155, 155, 155, 155, 69, 69, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 614 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450878 none CC1C(NC(=O)C2=CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 14, 47, 155, 155, 155, 155, 155, 2, 2, 2, 1, 1, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 14, 14, 155] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 266 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450878 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450878 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450878/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450878 Building REAL300024450879 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450879' /scratch/stefan/7786230/working/building/REAL300024450879 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450879 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450879/0 /scratch/stefan/7786230/working/building/REAL300024450879 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/781 `/scratch/stefan/7786230/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(CO)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450879/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450879 none CC1C(NC(=O)C2=CC=C(CO)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 420 conformations in input total number of sets (complete confs): 420 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 1, 11, 11, 11, 11, 11, 16, 16, 46, 67, 140, 140, 140, 140, 140, 11, 11, 11, 11, 11, 7, 1, 1, 8, 8, 24, 11, 11, 11, 11, 11, 11, 46, 46, 140] 420 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 12] set([0, 1, 2, 3, 5, 11, 13, 14, 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, 44, 45, 46]) total number of confs: 360 number of broken/clashed sets: 75 ./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: REAL300024450879 none CC1C(NC(=O)C2=CC=C(CO)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 420 conformations in input total number of sets (complete confs): 420 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 109, 109, 109, 140, 140, 140, 140, 140, 140, 95, 95, 95, 86, 40, 86, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 109, 140, 140, 140, 140, 420, 95, 95, 95, 95, 95, 95, 40, 40, 1] 420 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 825 number of broken/clashed sets: 75 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450879 none CC1C(NC(=O)C2=CC=C(CO)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 5, 12, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 420 conformations in input total number of sets (complete confs): 420 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 28, 11, 1, 1, 1, 1, 1, 3, 3, 15, 31, 95, 95, 95, 95, 95, 2, 2, 2, 1, 1, 4, 11, 11, 28, 28, 84, 1, 1, 1, 1, 1, 1, 15, 15, 95] 420 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 339 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450879 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450879 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450879/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450879 Building REAL300024450880 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450880' /scratch/stefan/7786230/working/building/REAL300024450880 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450880 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450880/0 /scratch/stefan/7786230/working/building/REAL300024450880 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/782 `/scratch/stefan/7786230/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)F) `REAL300024450880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450880/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450880 none CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 99, 99, 99, 57, 57, 57, 57, 57, 54, 45, 54, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201, 99, 57, 57, 57, 57, 57, 57, 57, 45, 45, 1, 57, 57, 57, 57, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45]) total number of confs: 632 number of broken/clashed sets: 85 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450880 none CC(=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 57, 57, 57, 57, 57, 1, 1, 30, 61, 61, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 57, 1, 2, 2, 2, 61] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 324 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450880 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450880 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450880/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450880 Building REAL300024450881 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450881' /scratch/stefan/7786230/working/building/REAL300024450881 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450881 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450881/0 /scratch/stefan/7786230/working/building/REAL300024450881 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/783 `/scratch/stefan/7786230/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450881/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450881 none CC1C(NC(=O)C2(C)CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 51, 101, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 51, 51, 201] 201 rigid atoms, others: [43, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 429 number of broken/clashed sets: 29 ./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: REAL300024450881 none CC1C(NC(=O)C2(C)CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 81, 81, 84, 84, 84, 201, 201, 201, 201, 201, 201, 81, 81, 81, 79, 41, 79, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 81, 81, 81, 41, 41, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 600 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450881 none CC1C(NC(=O)C2(C)CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 12, 28, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 81] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450881 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450881 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450881/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450881 Building REAL300024450882 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450882' /scratch/stefan/7786230/working/building/REAL300024450882 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450882 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450882/0 /scratch/stefan/7786230/working/building/REAL300024450882 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/784 `/scratch/stefan/7786230/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450882/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450882 none CC1C(NC(=O)C=CC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 14, 14, 14, 16, 16, 17, 17, 17, 17, 13, 13, 13, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 14, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 12, 12, 1] 17 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 53 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450882 none CC1C(NC(=O)C=CC[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 9, 9, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 5, 6, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 3, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 13] 17 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450882 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450882 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450882/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450882 Building REAL300024450883 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450883' /scratch/stefan/7786230/working/building/REAL300024450883 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450883 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450883/0 /scratch/stefan/7786230/working/building/REAL300024450883 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/785 `/scratch/stefan/7786230/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450883/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450883 none CCC[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 149, 83, 149, 149, 83, 83, 70, 70, 70, 70, 70, 65, 27, 65, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 447, 83, 70, 70, 70, 70, 70, 70, 70, 27, 27, 1, 70, 70, 70, 70] 603 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 1315 number of broken/clashed sets: 51 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450883 none CCC[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 29, 15, 3, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 70, 70, 70, 70, 70, 1, 1, 30, 30, 30, 30, 30, 30, 30, 45, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 70, 1, 2, 2, 2] 603 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 297 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450883 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450883 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450883/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450883 Building REAL300024450884 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450884' /scratch/stefan/7786230/working/building/REAL300024450884 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450884 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450884/0 /scratch/stefan/7786230/working/building/REAL300024450884 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/786 `/scratch/stefan/7786230/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1) `REAL300024450884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450884/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450884 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 36, 113, 113, 113, 113, 113, 1, 1, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 113, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 207 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: REAL300024450884 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 118, 118, 118, 113, 113, 113, 113, 113, 110, 48, 110, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 118, 113, 113, 113, 113, 113, 113, 113, 48, 48, 1, 113, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 631 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450884 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 9, 9, 9, 9, 9, 15, 15, 48, 101, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 48, 48, 201, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 428 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450884 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450884 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450884/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450884 Building REAL300024450885 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450885' /scratch/stefan/7786230/working/building/REAL300024450885 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450885 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450885/0 /scratch/stefan/7786230/working/building/REAL300024450885 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/787 `/scratch/stefan/7786230/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2COCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450885/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450885 none CC1C(NC(=O)CC2COCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 25, 25, 7, 25, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 51, 51, 88, 127, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 88, 88, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 544 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: REAL300024450885 none CC1C(NC(=O)CC2COCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 85, 85, 85, 199, 201, 201, 201, 201, 201, 70, 70, 70, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 85, 199, 199, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 28, 28, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 755 number of broken/clashed sets: 4 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450885 none CC1C(NC(=O)CC2COCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 19, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 10, 18, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 4, 19, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 10, 10, 70] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450885 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450885 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450885/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450885 Building REAL300024450886 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450886' /scratch/stefan/7786230/working/building/REAL300024450886 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450886 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450886/0 /scratch/stefan/7786230/working/building/REAL300024450886 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/788 `/scratch/stefan/7786230/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1) `REAL300024450886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450886/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450886 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3] 3 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 17 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: REAL300024450886 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3] 3 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 7 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450886 none CC(C)C1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [1, 3, 4, 49, 50, 51, 52, 24, 25, 26] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 16 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450886 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450886 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450886/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450886 Building REAL300024450887 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450887' /scratch/stefan/7786230/working/building/REAL300024450887 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450887 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450887/0 /scratch/stefan/7786230/working/building/REAL300024450887 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/789 `/scratch/stefan/7786230/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450887/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450887 none CNC(=O)N[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 91, 180, 180, 91, 91, 87, 87, 87, 87, 87, 85, 30, 85, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 180, 180, 180, 91, 87, 87, 87, 87, 87, 87, 87, 30, 30, 1, 87, 87, 87, 87] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 762 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450887 none CNC(=O)N[C@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 22, 22, 22, 13, 3, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 87, 87, 87, 87, 87, 1, 1, 34, 34, 34, 34, 22, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 1, 2, 2, 2] 201 rigid atoms, others: [43, 47, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 262 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450887 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450887 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450887/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450887 Building REAL300024450888 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450888' /scratch/stefan/7786230/working/building/REAL300024450888 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450888 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450888/0 /scratch/stefan/7786230/working/building/REAL300024450888 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/790 `/scratch/stefan/7786230/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450888/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450888 none CC1C(NC(=O)CC2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 20, 20, 9, 20, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 38, 38, 84, 127, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 20, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 84, 84, 201] 201 rigid atoms, others: [11, 38, 6, 7, 8, 9, 10, 39, 12, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 547 number of broken/clashed sets: 10 ./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: REAL300024450888 none CC1C(NC(=O)CC2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 106, 106, 106, 119, 119, 119, 175, 201, 201, 201, 201, 201, 106, 106, 106, 101, 31, 101, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 119, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 106, 31, 31, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 722 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450888 none CC1C(NC(=O)CC2(C)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 13, 30, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 3, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 13, 13, 106] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450888 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450888 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450888/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450888 Building REAL300024450889 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450889' /scratch/stefan/7786230/working/building/REAL300024450889 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450889 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450889/0 /scratch/stefan/7786230/working/building/REAL300024450889 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/791 `/scratch/stefan/7786230/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1) `REAL300024450889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450889/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450889 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 28, 87, 87, 87, 87, 87, 1, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 87, 1, 2, 2, 2, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 20 ./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: REAL300024450889 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 94, 94, 94, 87, 87, 87, 87, 87, 84, 47, 84, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 94, 87, 87, 87, 87, 87, 87, 87, 47, 47, 1, 87, 87, 87, 87, 201, 201, 201, 201] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 459 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450889 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N(C)C=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 13, 13, 13, 13, 13, 19, 19, 51, 95, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 13, 51, 51, 201, 13, 13, 13, 13, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 450 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450889 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450889 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450889/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450889 Building REAL300024450890 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450890' /scratch/stefan/7786230/working/building/REAL300024450890 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450890 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450890/0 /scratch/stefan/7786230/working/building/REAL300024450890 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/792 `/scratch/stefan/7786230/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450890/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450890 none CC1C(NC(=O)CC2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 25, 25, 5, 25, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 45, 45, 88, 130, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 25, 5, 5, 1, 32, 32, 32, 32, 32, 32, 88, 88, 201] 201 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 544 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: REAL300024450890 none CC1C(NC(=O)CC2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 77, 77, 77, 105, 105, 105, 187, 201, 201, 201, 201, 77, 77, 77, 74, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 105, 187, 187, 201, 77, 77, 77, 77, 77, 77, 29, 29, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 757 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450890 none CC1C(NC(=O)CC2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 21, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 4, 21, 21, 32, 1, 1, 1, 1, 1, 1, 10, 10, 77] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450890 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450890 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450890/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450890 Building REAL300024450891 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450891' /scratch/stefan/7786230/working/building/REAL300024450891 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450891 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450891/0 /scratch/stefan/7786230/working/building/REAL300024450891 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/793 `/scratch/stefan/7786230/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12) `REAL300024450891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450891/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450891 none CO[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 28, 88, 88, 88, 88, 88, 1, 1, 13, 13, 13, 26, 26, 26, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 88, 1, 2, 2, 2, 13, 13] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 198 number of broken/clashed sets: 35 ./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: REAL300024450891 none CO[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 107, 107, 107, 88, 88, 88, 88, 88, 83, 38, 83, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 107, 88, 88, 88, 88, 88, 88, 88, 38, 38, 1, 88, 88, 88, 88, 201, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 488 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450891 none CO[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 19, 19, 67, 104, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 5, 5, 5, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 67, 67, 201, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 50, 26, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 473 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450891 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450891 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450891/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450891 Building REAL300024450892 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450892' /scratch/stefan/7786230/working/building/REAL300024450892 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450892 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450892/0 /scratch/stefan/7786230/working/building/REAL300024450892 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/794 `/scratch/stefan/7786230/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450892/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450892 none CC1C(NC(=O)CC2=NN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 39, 39, 86, 121, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 22, 5, 5, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31, 86, 86, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47]) total number of confs: 539 number of broken/clashed sets: 8 ./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: REAL300024450892 none CC1C(NC(=O)CC2=NN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 93, 93, 93, 121, 121, 121, 194, 201, 201, 201, 201, 201, 93, 93, 93, 87, 29, 87, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 121, 194, 194, 201, 201, 201, 201, 93, 93, 93, 93, 93, 93, 29, 29, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 719 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450892 none CC1C(NC(=O)CC2=NN=CN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 20, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 11, 24, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 4, 20, 20, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 11, 11, 93] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450892 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450892 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450892/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450892 Building REAL300024450893 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450893' /scratch/stefan/7786230/working/building/REAL300024450893 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450893 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450893/0 /scratch/stefan/7786230/working/building/REAL300024450893 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/795 `/scratch/stefan/7786230/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450893/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450893 none CCC1=NON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 27, 113, 113, 113, 113, 113, 1, 1, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 113, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 260 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: REAL300024450893 none CCC1=NON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 158, 158, 158, 158, 158, 140, 140, 140, 113, 113, 113, 113, 113, 107, 31, 107, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 140, 113, 113, 113, 113, 113, 113, 113, 31, 31, 1, 113, 113, 113, 113] 201 rigid atoms, others: [42, 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, 43, 44, 45, 46]) total number of confs: 717 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450893 none CCC1=NON=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 15, 15, 48, 79, 158, 158, 158, 158, 158, 10, 10, 6, 6, 6, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 48, 48, 158, 10, 10, 10, 10] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 375 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450893 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450893 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450893/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450893 Building REAL300024450894 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450894' /scratch/stefan/7786230/working/building/REAL300024450894 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450894 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450894/0 /scratch/stefan/7786230/working/building/REAL300024450894 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/796 `/scratch/stefan/7786230/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450894/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450894 none CC1C(NC(=O)CC2=NSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 15, 15, 18, 18, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 11, 4, 4, 1, 13, 13, 13, 13, 13, 13, 18, 18, 24] 24 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 14 ./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: REAL300024450894 none CC1C(NC(=O)CC2=NSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 11, 11, 11, 16, 24, 24, 24, 24, 9, 9, 9, 9, 8, 9, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 11, 16, 16, 24, 9, 9, 9, 9, 9, 9, 8, 8, 1] 24 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450894 none CC1C(NC(=O)CC2=NSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 8, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 8, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 5, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 3, 8, 8, 13, 1, 1, 1, 1, 1, 1, 5, 5, 9] 24 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450894 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450894 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450894/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450894 Building REAL300024450895 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450895' /scratch/stefan/7786230/working/building/REAL300024450895 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450895 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450895/0 /scratch/stefan/7786230/working/building/REAL300024450895 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/797 `/scratch/stefan/7786230/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450895/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450895 none C=CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 142, 77, 142, 142, 56, 56, 56, 45, 45, 45, 45, 45, 43, 23, 43, 12, 1, 1, 1, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 142, 77, 77, 56, 45, 45, 45, 45, 45, 45, 45, 23, 23, 1, 45, 45, 45, 45] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 907 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450895 none C=CCC(C)(C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 6, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 45, 45, 45, 45, 45, 1, 1, 39, 39, 39, 28, 28, 18, 18, 18, 18, 18, 18, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 45, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 254 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450895 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450895 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450895/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450895 Building REAL300024450896 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450896' /scratch/stefan/7786230/working/building/REAL300024450896 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450896 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450896/0 /scratch/stefan/7786230/working/building/REAL300024450896 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/798 `/scratch/stefan/7786230/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450896/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450896 none CCC(C)(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 94, 199, 199, 201, 94, 94, 51, 51, 51, 51, 51, 50, 45, 50, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 199, 199, 199, 201, 201, 201, 94, 51, 51, 51, 51, 51, 51, 51, 45, 45, 1, 51, 51, 51, 51] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 803 number of broken/clashed sets: 65 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450896 none CCC(C)(OC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 24, 6, 24, 24, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 51, 51, 51, 51, 51, 1, 1, 31, 31, 31, 31, 31, 24, 24, 24, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 51, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 249 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450896 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450896 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450896/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450896 Building REAL300024450897 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450897' /scratch/stefan/7786230/working/building/REAL300024450897 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450897 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450897/0 /scratch/stefan/7786230/working/building/REAL300024450897 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/799 `/scratch/stefan/7786230/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450897/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450897 none CC(C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 6, 7, 5, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 18, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 21 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 39 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450897 none CC(C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 3, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 15, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 21 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450897 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450897 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450897/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450897 Building REAL300024450898 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450898' /scratch/stefan/7786230/working/building/REAL300024450898 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450898 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450898/0 /scratch/stefan/7786230/working/building/REAL300024450898 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/800 `/scratch/stefan/7786230/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450898/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450898 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 21 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: REAL300024450898 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 11 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450898 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450898 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450898 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450898/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450898 Building REAL300024450899 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450899' /scratch/stefan/7786230/working/building/REAL300024450899 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450899 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450899/0 /scratch/stefan/7786230/working/building/REAL300024450899 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/801 `/scratch/stefan/7786230/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450899/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450899 none CC(CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 156, 157, 112, 112, 112, 88, 88, 88, 88, 88, 73, 31, 73, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 157, 157, 112, 88, 88, 88, 88, 88, 88, 88, 31, 31, 1, 88, 88, 88, 88, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 874 number of broken/clashed sets: 126 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450899 none CC(CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 14, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 27, 88, 88, 88, 88, 88, 1, 1, 25, 31, 31, 31, 25, 25, 25, 25, 16, 16, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 88, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 12, 47, 43, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 302 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450899 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450899 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450899/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450899 Building REAL300024450900 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450900' /scratch/stefan/7786230/working/building/REAL300024450900 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450900 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450900/0 /scratch/stefan/7786230/working/building/REAL300024450900 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/802 `/scratch/stefan/7786230/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450900/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450900 none CC1C(NC(=O)C2=CN=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 40, 60, 100, 100, 100, 100, 100, 9, 9, 9, 9, 9, 3, 1, 1, 9, 9, 9, 9, 9, 9, 40, 40, 100] 100 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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: 255 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: REAL300024450900 none CC1C(NC(=O)C2=CN=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 100, 100, 100, 100, 100, 100, 100, 100, 100, 75, 75, 75, 69, 36, 69, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 100, 100, 100, 75, 75, 75, 75, 75, 75, 36, 36, 1] 100 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450900 none CC1C(NC(=O)C2=CN=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 16, 31, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 6, 9, 9, 1, 1, 1, 1, 1, 1, 16, 16, 75] 100 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 35, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 41, 42, 43]) total number of confs: 167 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450900 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450900 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450900/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450900 Building REAL300024450901 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450901' /scratch/stefan/7786230/working/building/REAL300024450901 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450901 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450901/0 /scratch/stefan/7786230/working/building/REAL300024450901 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/803 `/scratch/stefan/7786230/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450901/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450901 none CC(C)C(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4] 18 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 35 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450901 none CC(C)C(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 2, 4, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 1, 2, 2, 2] 18 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450901 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450901 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450901/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450901 Building REAL300024450902 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450902' /scratch/stefan/7786230/working/building/REAL300024450902 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450902 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450902/0 /scratch/stefan/7786230/working/building/REAL300024450902 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/804 `/scratch/stefan/7786230/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450902/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450902 none CCOC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 175, 175, 97, 97, 97, 93, 93, 93, 93, 93, 83, 27, 83, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 175, 175, 97, 93, 93, 93, 93, 93, 93, 93, 27, 27, 1, 93, 93, 93, 93] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 573 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450902 none CCOC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 23, 93, 93, 93, 93, 93, 1, 1, 39, 39, 39, 39, 39, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 93, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450902 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450902 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450902/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450902 Building REAL300024450903 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450903' /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450903 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450903/0 /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/805 `/scratch/stefan/7786230/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450903/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CCN1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 76, 76, 76, 76, 76, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 76, 1, 2, 2, 2] 88 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 161 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: REAL300024450903 none CCN1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 88, 88, 88, 88, 82, 82, 82, 76, 76, 76, 76, 76, 69, 39, 69, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 82, 76, 76, 76, 76, 76, 76, 76, 39, 39, 1, 76, 76, 76, 76] 88 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 296 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CCN1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 8, 8, 30, 46, 88, 88, 88, 88, 88, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 30, 30, 88, 6, 6, 6, 6] 88 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450903/1 /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/806 `/scratch/stefan/7786230/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450903.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450903/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CC[N@@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 65, 65, 65, 65, 65, 1, 1, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 65, 1, 2, 2, 2] 182 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 34 ./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: REAL300024450903 none CC[N@@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 182, 182, 182, 182, 182, 131, 131, 131, 65, 65, 65, 65, 65, 64, 34, 64, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 131, 65, 65, 65, 65, 65, 65, 65, 34, 34, 1, 65, 65, 65, 65] 182 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 613 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CC[N@@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 37, 37, 85, 112, 182, 182, 182, 182, 182, 23, 23, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 85, 85, 182, 23, 23, 23, 23] 182 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36] set([0, 8, 9, 10, 11, 12, 13, 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 514 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450903/2 /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/807 `/scratch/stefan/7786230/working/3D/807' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450903.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450903/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CC[N@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 1, 1, 31, 31, 31, 31, 31, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 58, 1, 2, 2, 2] 148 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 225 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: REAL300024450903 none CC[N@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 148, 109, 109, 109, 58, 58, 58, 58, 58, 58, 32, 58, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 109, 58, 58, 58, 58, 58, 58, 58, 32, 32, 1, 58, 58, 58, 58] 148 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 494 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450903 none CC[N@H+]1CCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 19, 19, 19, 31, 31, 68, 88, 148, 148, 148, 148, 148, 19, 19, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 68, 68, 148, 19, 19, 19, 19] 148 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36] set([0, 8, 9, 10, 11, 12, 13, 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 407 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450903 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450903 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450903/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450903/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450903/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450903 Building REAL300024450904 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450904' /scratch/stefan/7786230/working/building/REAL300024450904 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450904 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450904/0 /scratch/stefan/7786230/working/building/REAL300024450904 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/808 `/scratch/stefan/7786230/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450904/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450904 none CC1C(NC(=O)CC2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 16, 16, 6, 16, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 32, 32, 85, 132, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 85, 85, 201] 603 rigid atoms, others: [43, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 535 number of broken/clashed sets: 82 ./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: REAL300024450904 none CC1C(NC(=O)CC2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [116, 116, 116, 116, 129, 129, 129, 193, 201, 201, 201, 201, 201, 116, 116, 116, 103, 30, 103, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 129, 193, 193, 603, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 116, 30, 30, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1321 number of broken/clashed sets: 82 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450904 none CC1C(NC(=O)CC2(O)CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 3, 3, 12, 29, 116, 116, 116, 116, 116, 2, 2, 2, 1, 1, 3, 14, 14, 66, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 12, 12, 116] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 325 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450904 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450904 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450904/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450904 Building REAL300024450905 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450905' /scratch/stefan/7786230/working/building/REAL300024450905 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450905 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450905/0 /scratch/stefan/7786230/working/building/REAL300024450905 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/809 `/scratch/stefan/7786230/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450905/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450905 none CC1C(NC(=O)C2CCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 67, 118, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 67, 67, 201] 603 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 499 number of broken/clashed sets: 42 ./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: REAL300024450905 none CC1C(NC(=O)C2CCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [112, 112, 112, 112, 125, 125, 125, 201, 201, 201, 201, 201, 112, 112, 112, 109, 49, 109, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 125, 201, 201, 201, 201, 201, 201, 201, 201, 603, 112, 112, 112, 112, 112, 112, 49, 49, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1235 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450905 none CC1C(NC(=O)C2CCCC2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 13, 37, 112, 112, 112, 112, 112, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 33, 1, 1, 1, 1, 1, 1, 13, 13, 112] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450905 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450905 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450905/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450905 Building REAL300024450906 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450906' /scratch/stefan/7786230/working/building/REAL300024450906 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450906 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450906/0 /scratch/stefan/7786230/working/building/REAL300024450906 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/810 `/scratch/stefan/7786230/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450906/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450906 none C[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 163, 201, 201, 163, 163, 152, 152, 152, 152, 152, 144, 54, 144, 13, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 603, 163, 152, 152, 152, 152, 152, 152, 152, 54, 54, 1, 152, 152, 152, 152] 603 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] 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, 39, 40, 41, 42]) total number of confs: 1297 number of broken/clashed sets: 60 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450906 none C[C@@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 43, 152, 152, 152, 152, 152, 1, 1, 15, 15, 15, 45, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 152, 1, 2, 2, 2] 603 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 329 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450906 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450906 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450906/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450906 Building REAL300024450907 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450907' /scratch/stefan/7786230/working/building/REAL300024450907 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450907 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450907/0 /scratch/stefan/7786230/working/building/REAL300024450907 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/811 `/scratch/stefan/7786230/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450907/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450907 none CSSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 105, 53, 53, 53, 43, 43, 43, 43, 43, 41, 22, 41, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 201, 201, 201, 105, 105, 53, 43, 43, 43, 43, 43, 43, 43, 22, 22, 1, 43, 43, 43, 43] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 572 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450907 none CSSCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 40, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 43, 43, 43, 43, 43, 1, 1, 48, 48, 48, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450907 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450907 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450907/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450907 Building REAL300024450908 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450908' /scratch/stefan/7786230/working/building/REAL300024450908 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450908 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450908/0 /scratch/stefan/7786230/working/building/REAL300024450908 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/812 `/scratch/stefan/7786230/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450908/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450908 none CC1C(NC(=O)CC(O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 95, 95, 95, 112, 112, 112, 186, 199, 199, 201, 201, 95, 95, 95, 87, 31, 87, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 112, 186, 186, 199, 597, 201, 201, 95, 95, 95, 95, 95, 95, 31, 31, 1] 603 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1365 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450908 none CC1C(NC(=O)CC(O)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 14, 26, 26, 46, 46, 1, 1, 1, 1, 1, 3, 3, 12, 26, 95, 95, 95, 95, 95, 2, 2, 2, 1, 1, 3, 14, 14, 26, 78, 46, 46, 1, 1, 1, 1, 1, 1, 12, 12, 95] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450908 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450908 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450908/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450908 Building REAL300024450909 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450909' /scratch/stefan/7786230/working/building/REAL300024450909 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450909 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450909/0 /scratch/stefan/7786230/working/building/REAL300024450909 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/813 `/scratch/stefan/7786230/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450909/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450909 none CCC(C)=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 124, 83, 124, 83, 83, 61, 61, 61, 61, 61, 58, 24, 58, 12, 1, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 124, 83, 61, 61, 61, 61, 61, 61, 61, 24, 24, 1, 61, 61, 61, 61] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 888 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450909 none CCC(C)=C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 13, 13, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 61, 61, 61, 61, 61, 1, 1, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 61, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450909 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450909 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450909/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450909 Building REAL300024450910 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450910' /scratch/stefan/7786230/working/building/REAL300024450910 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450910 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450910/0 /scratch/stefan/7786230/working/building/REAL300024450910 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/814 `/scratch/stefan/7786230/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024450910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450910/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450910 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 19 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: REAL300024450910 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450910 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450910 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450910 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450910/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450910 Building REAL300024450911 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450911' /scratch/stefan/7786230/working/building/REAL300024450911 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450911 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450911/0 /scratch/stefan/7786230/working/building/REAL300024450911 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/815 `/scratch/stefan/7786230/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450911/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450911 none CC1C(NC(=O)CCC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 59, 59, 59, 72, 72, 72, 167, 167, 201, 201, 201, 59, 59, 59, 56, 35, 56, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 72, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 603, 59, 59, 59, 59, 59, 59, 35, 35, 1] 603 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1477 number of broken/clashed sets: 96 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450911 none CC1C(NC(=O)CCC(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 17, 17, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 8, 14, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 41, 41, 41, 41, 41, 41, 123, 1, 1, 1, 1, 1, 1, 8, 8, 59] 603 rigid atoms, others: [0, 1, 2, 3, 16, 44, 43, 12, 13, 14, 15, 48, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 378 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450911 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450911 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450911/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450911 Building REAL300024450912 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450912' /scratch/stefan/7786230/working/building/REAL300024450912 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450912 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450912/0 /scratch/stefan/7786230/working/building/REAL300024450912 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/816 `/scratch/stefan/7786230/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(CO)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450912/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450912 none CC1C(NC(=O)C(CO)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 597 conformations in input total number of sets (complete confs): 597 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 170, 170, 170, 199, 199, 199, 199, 199, 199, 92, 92, 92, 90, 60, 90, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 170, 199, 199, 199, 597, 199, 199, 199, 199, 199, 199, 199, 199, 199, 92, 92, 92, 92, 92, 92, 60, 60, 1] 597 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1303 number of broken/clashed sets: 573 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450912 none CC1C(NC(=O)C(CO)C(C)(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 597 conformations in input total number of sets (complete confs): 597 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 13, 21, 13, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 11, 22, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 6, 13, 21, 21, 63, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 92] 597 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 316 number of broken/clashed sets: 573 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450912 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450912 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450912/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450912 Building REAL300024450913 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450913' /scratch/stefan/7786230/working/building/REAL300024450913 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450913 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450913/0 /scratch/stefan/7786230/working/building/REAL300024450913 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/817 `/scratch/stefan/7786230/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)C=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450913/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450913 none CC1C(NC(=O)C2=CC(=O)C=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 23, 35, 48, 48, 48, 48, 48, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 23, 23, 48] 48 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 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: REAL300024450913 none CC1C(NC(=O)C2=CC(=O)C=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 37, 37, 38, 38, 38, 48, 48, 48, 48, 48, 48, 37, 37, 37, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 38, 48, 48, 48, 48, 37, 37, 37, 37, 37, 37, 25, 25, 1] 48 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450913 none CC1C(NC(=O)C2=CC(=O)C=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 3, 3, 12, 19, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 3, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 37] 48 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450913 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450913 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450913/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450913 Building REAL300024450914 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450914' /scratch/stefan/7786230/working/building/REAL300024450914 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450914 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450914/0 /scratch/stefan/7786230/working/building/REAL300024450914 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/818 `/scratch/stefan/7786230/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=O)NC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450914/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450914 none CC1CC(=O)NC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 48, 174, 174, 174, 174, 174, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 174, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 281 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: REAL300024450914 none CC1CC(=O)NC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 187, 187, 187, 174, 174, 174, 174, 174, 171, 73, 171, 13, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 187, 174, 174, 174, 174, 174, 174, 174, 73, 73, 1, 174, 174, 174, 174] 201 rigid atoms, others: [45, 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, 43, 44, 46, 47, 48, 49]) total number of confs: 636 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450914 none CC1CC(=O)NC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 8, 8, 8, 8, 8, 12, 12, 44, 104, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 44, 44, 201, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 415 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450914 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450914 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450914/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450914 Building REAL300024450915 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450915' /scratch/stefan/7786230/working/building/REAL300024450915 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450915 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450915/0 /scratch/stefan/7786230/working/building/REAL300024450915 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/819 `/scratch/stefan/7786230/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450915/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450915 none CC1C(NC(=O)C2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 15, 15, 49, 109, 201, 201, 201, 201, 201, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 8, 8, 49, 49, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 25 ./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: REAL300024450915 none CC1C(NC(=O)C2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [131, 131, 131, 131, 148, 148, 148, 201, 201, 201, 201, 131, 131, 131, 129, 57, 129, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 148, 201, 201, 131, 131, 131, 131, 131, 131, 57, 57, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 574 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450915 none CC1C(NC(=O)C2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 13, 41, 131, 131, 131, 131, 131, 2, 2, 2, 1, 1, 3, 8, 8, 1, 1, 1, 1, 1, 1, 13, 13, 131] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 228 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450915 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450915 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450915/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450915 Building REAL300024450916 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450916' /scratch/stefan/7786230/working/building/REAL300024450916 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450916 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450916/0 /scratch/stefan/7786230/working/building/REAL300024450916 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/820 `/scratch/stefan/7786230/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450916/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450916 none CCC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [33, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 25, 83, 83, 83, 83, 83, 1, 1, 12, 33, 33, 33, 33, 33, 12, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 83, 1, 2, 2, 2, 12] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 262 number of broken/clashed sets: 38 ./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: REAL300024450916 none CCC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 130, 130, 130, 130, 117, 117, 117, 83, 83, 83, 83, 83, 80, 40, 80, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 130, 201, 201, 201, 201, 201, 130, 117, 83, 83, 83, 83, 83, 83, 83, 40, 40, 1, 83, 83, 83, 83, 130] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 839 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450916 none CCC1=NC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 18, 18, 47, 66, 130, 130, 130, 130, 130, 12, 12, 1, 9, 9, 9, 9, 9, 1, 6, 12, 12, 12, 12, 12, 12, 12, 47, 47, 130, 12, 12, 12, 12, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 340 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450916 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450916 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450916/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450916 Building REAL300024450917 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450917' /scratch/stefan/7786230/working/building/REAL300024450917 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450917 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450917/0 /scratch/stefan/7786230/working/building/REAL300024450917 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/821 `/scratch/stefan/7786230/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450917/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450917 none CCC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [25, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 31, 112, 112, 112, 112, 112, 1, 1, 9, 25, 25, 25, 25, 25, 9, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 112, 1, 2, 2, 2] 192 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47]) total number of confs: 276 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: REAL300024450917 none CCC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 151, 151, 151, 151, 150, 150, 150, 112, 112, 112, 112, 112, 101, 42, 101, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 151, 192, 192, 192, 192, 192, 151, 150, 112, 112, 112, 112, 112, 112, 112, 42, 42, 1, 112, 112, 112, 112] 192 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 739 number of broken/clashed sets: 37 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450917 none CCC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 14, 14, 44, 68, 151, 151, 151, 151, 151, 9, 9, 1, 9, 9, 9, 9, 9, 1, 3, 9, 9, 9, 9, 9, 9, 9, 44, 44, 151, 9, 9, 9, 9] 192 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 354 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450917 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450917/1 /scratch/stefan/7786230/working/building/REAL300024450917 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/822 `/scratch/stefan/7786230/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450917.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450917/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450917 none CCC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [18, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 54, 54, 54, 54, 54, 1, 1, 7, 18, 18, 18, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 1, 2, 2, 2, 7] 103 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 22 ./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: REAL300024450917 none CCC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [103, 66, 66, 66, 66, 66, 66, 66, 54, 54, 54, 54, 54, 49, 33, 49, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 66, 103, 103, 103, 103, 103, 66, 54, 54, 54, 54, 54, 54, 54, 33, 33, 1, 54, 54, 54, 54, 66] 103 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 447 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450917 none CCC1=NN=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 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: [7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 9, 9, 25, 37, 66, 66, 66, 66, 66, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 25, 25, 66, 7, 7, 7, 7, 1] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450917 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450917 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450917/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450917/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450917 Building REAL300024450918 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450918' /scratch/stefan/7786230/working/building/REAL300024450918 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450918 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450918/0 /scratch/stefan/7786230/working/building/REAL300024450918 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/823 `/scratch/stefan/7786230/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450918/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450918 none CC1C(NC(=O)CC2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 31, 31, 87, 135, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 87, 87, 201] 603 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 542 number of broken/clashed sets: 96 ./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: REAL300024450918 none CC1C(NC(=O)CC2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [129, 129, 129, 129, 141, 141, 141, 198, 201, 201, 201, 201, 201, 129, 129, 129, 111, 30, 111, 13, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 141, 198, 198, 603, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 129, 30, 30, 1] 603 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1300 number of broken/clashed sets: 96 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450918 none CC1C(NC(=O)CC2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 14, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 4, 13, 31, 129, 129, 129, 129, 129, 2, 2, 2, 1, 1, 4, 14, 14, 57, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 13, 13, 129] 603 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 322 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450918 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450918 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450918/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450918 Building REAL300024450919 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450919' /scratch/stefan/7786230/working/building/REAL300024450919 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450919 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450919/0 /scratch/stefan/7786230/working/building/REAL300024450919 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/824 `/scratch/stefan/7786230/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450919/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450919 none CC1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 3, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 29, 80, 80, 80, 80, 80, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 80, 1, 2, 2, 2, 10, 10] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 169 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: REAL300024450919 none CC1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 201, 84, 84, 80, 80, 80, 80, 80, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 80, 80, 80, 80, 80, 80, 80, 39, 39, 1, 80, 80, 80, 80, 201, 201] 201 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 597 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450919 none CC1CC(C)(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 10, 10, 10, 10, 10, 15, 15, 51, 100, 201, 201, 201, 201, 201, 10, 10, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 7, 10, 10, 10, 10, 10, 10, 10, 51, 51, 201, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 50, 51, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 444 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450919 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450919 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450919/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450919 Building REAL300024450920 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450920' /scratch/stefan/7786230/working/building/REAL300024450920 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450920 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450920/0 /scratch/stefan/7786230/working/building/REAL300024450920 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/825 `/scratch/stefan/7786230/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450920/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450920 none CC1C(NC(=O)CC2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 35, 35, 78, 124, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 20, 5, 5, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 78, 78, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47]) total number of confs: 529 number of broken/clashed sets: 9 ./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: REAL300024450920 none CC1C(NC(=O)CC2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [74, 74, 74, 74, 89, 89, 89, 185, 201, 201, 201, 201, 201, 74, 74, 74, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 89, 185, 185, 201, 201, 201, 201, 74, 74, 74, 74, 74, 74, 28, 28, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 705 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450920 none CC1C(NC(=O)CC2=NC=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 17, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 12, 21, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 3, 17, 17, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 12, 12, 74] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450920 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450920 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450920/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450920 Building REAL300024450921 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450921' /scratch/stefan/7786230/working/building/REAL300024450921 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450921 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450921/0 /scratch/stefan/7786230/working/building/REAL300024450921 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/826 `/scratch/stefan/7786230/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450921/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450921 none CNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 116, 116, 116, 86, 86, 86, 86, 86, 81, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 197, 197, 116, 86, 86, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86, 86, 86] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 803 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450921 none CNC(=O)CCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 16, 27, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 86, 86, 86, 86, 86, 1, 1, 27, 27, 27, 27, 16, 16, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 86, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450921 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450921 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450921/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450921 Building REAL300024450922 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450922' /scratch/stefan/7786230/working/building/REAL300024450922 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450922 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450922/0 /scratch/stefan/7786230/working/building/REAL300024450922 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/827 `/scratch/stefan/7786230/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450922/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450922 none CC1C(NC(=O)CCC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 29, 29, 8, 29, 4, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 44, 44, 95, 138, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 29, 8, 8, 4, 4, 1, 1, 38, 38, 38, 38, 38, 38, 95, 95, 201] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 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, 45, 46, 47]) total number of confs: 594 number of broken/clashed sets: 38 ./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: REAL300024450922 none CC1C(NC(=O)CCC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 36, 36, 47, 47, 47, 112, 118, 201, 201, 201, 201, 36, 36, 36, 34, 25, 34, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 47, 112, 112, 118, 118, 201, 201, 36, 36, 36, 36, 36, 36, 25, 25, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 639 number of broken/clashed sets: 38 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450922 none CC1C(NC(=O)CCC2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 20, 38, 38, 38, 38, 1, 1, 1, 1, 1, 3, 3, 7, 11, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 3, 15, 15, 20, 20, 38, 38, 1, 1, 1, 1, 1, 1, 7, 7, 36] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450922 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450922 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450922/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450922 Building REAL300024450923 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450923' /scratch/stefan/7786230/working/building/REAL300024450923 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450923 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450923/0 /scratch/stefan/7786230/working/building/REAL300024450923 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/828 `/scratch/stefan/7786230/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450923/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450923 none CC1C(NC(=O)CC2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 20, 21, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 8, 3, 3, 1, 1, 12, 12, 12, 12, 12, 12, 20, 20, 24] 24 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 7 ./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: REAL300024450923 none CC1C(NC(=O)CC2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 10, 10, 10, 14, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 14, 14, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 1] 24 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450923 none CC1C(NC(=O)CC2=CSN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 14, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 6, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 3, 6, 6, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8] 24 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450923 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450923 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450923/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450923 Building REAL300024450924 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450924' /scratch/stefan/7786230/working/building/REAL300024450924 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450924 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450924/0 /scratch/stefan/7786230/working/building/REAL300024450924 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/829 `/scratch/stefan/7786230/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450924/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450924 none C=CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 178, 114, 114, 114, 80, 80, 80, 80, 80, 80, 42, 80, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 178, 182, 182, 182, 201, 201, 201, 201, 201, 178, 114, 80, 80, 80, 80, 80, 80, 80, 42, 42, 1, 80, 80, 80, 80, 182, 182, 182, 182, 182, 182] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 870 number of broken/clashed sets: 110 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450924 none C=CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 19, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 80, 80, 80, 80, 80, 1, 1, 9, 12, 12, 12, 30, 30, 30, 19, 19, 9, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 80, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 260 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450924 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450924 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450924/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450924 Building REAL300024450925 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450925' /scratch/stefan/7786230/working/building/REAL300024450925 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450925 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450925/0 /scratch/stefan/7786230/working/building/REAL300024450925 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/830 `/scratch/stefan/7786230/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450925/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450925 none CC1C(NC(=O)CCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 33, 33, 41, 41, 41, 162, 181, 201, 201, 33, 33, 33, 32, 21, 32, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 41, 162, 162, 201, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 33, 21, 21, 1] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46]) total number of confs: 934 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450925 none CC1C(NC(=O)CCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 17, 21, 42, 1, 1, 1, 1, 1, 3, 3, 6, 10, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 3, 13, 13, 21, 21, 21, 21, 42, 42, 1, 1, 1, 1, 1, 1, 6, 6, 33] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 11, 12, 13, 14, 44, 43, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 282 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450925 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450925 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450925/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450925 Building REAL300024450926 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450926' /scratch/stefan/7786230/working/building/REAL300024450926 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450926 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450926/0 /scratch/stefan/7786230/working/building/REAL300024450926 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/831 `/scratch/stefan/7786230/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450926/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450926 none CC1C(NC(=O)C=CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 99, 99, 99, 156, 156, 156, 83, 83, 83, 79, 40, 79, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 99, 156, 156, 156, 156, 468, 83, 83, 83, 83, 83, 83, 40, 40, 1] 468 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 1000 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450926 none CC1C(NC(=O)C=CCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 13, 13, 31, 1, 1, 1, 1, 1, 3, 3, 11, 23, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 4, 13, 13, 31, 31, 93, 1, 1, 1, 1, 1, 1, 11, 11, 83] 468 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450926 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450926 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450926/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450926 Building REAL300024450927 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450927' /scratch/stefan/7786230/working/building/REAL300024450927 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450927 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450927/0 /scratch/stefan/7786230/working/building/REAL300024450927 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/832 `/scratch/stefan/7786230/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CO)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450927/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450927 none CC1C(NC(=O)C2(CO)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 6, 6, 1, 6, 1, 1, 6, 1, 1, 1, 1, 19, 19, 19, 19, 19, 28, 28, 62, 95, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 62, 62, 201] 603 rigid atoms, others: [4, 37, 6, 7, 40, 9, 10, 11, 12, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 492 number of broken/clashed sets: 240 ./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: REAL300024450927 none CC1C(NC(=O)C2(CO)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 70, 70, 70, 124, 124, 124, 201, 201, 201, 201, 201, 201, 70, 70, 70, 69, 52, 69, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 124, 201, 201, 603, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 52, 52, 1] 603 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1267 number of broken/clashed sets: 240 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450927 none CC1C(NC(=O)C2(CO)CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 19, 35, 19, 19, 19, 19, 1, 1, 1, 1, 1, 3, 3, 10, 16, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 6, 35, 35, 105, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 10, 10, 70] 603 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 349 number of broken/clashed sets: 240 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450927 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450927 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450927/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450927 Building REAL300024450928 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450928' /scratch/stefan/7786230/working/building/REAL300024450928 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450928 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450928/0 /scratch/stefan/7786230/working/building/REAL300024450928 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/833 `/scratch/stefan/7786230/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450928/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450928 none CCC(C)CC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 163, 76, 163, 76, 76, 59, 59, 59, 59, 59, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163, 76, 59, 59, 59, 59, 59, 59, 59, 28, 28, 1, 59, 59, 59, 59] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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, 53, 54, 55, 56]) total number of confs: 845 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450928 none CCC(C)CC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 26, 32, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 59, 59, 59, 59, 59, 1, 1, 40, 40, 40, 40, 40, 32, 32, 32, 32, 26, 26, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 59, 1, 2, 2, 2] 201 rigid atoms, others: [43, 15, 9, 10, 11, 12, 45, 46, 44, 48, 49, 14, 25, 26, 47, 13, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 299 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450928 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450928 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450928/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450928 Building REAL300024450929 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450929' /scratch/stefan/7786230/working/building/REAL300024450929 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450929 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450929/0 /scratch/stefan/7786230/working/building/REAL300024450929 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/834 `/scratch/stefan/7786230/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)N2C=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450929/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450929 none CC1C(NC(=O)C(F)N2C=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 30, 30, 11, 30, 1, 11, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 53, 53, 96, 130, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 30, 11, 1, 1, 1, 39, 39, 39, 39, 39, 39, 96, 96, 201] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 566 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: REAL300024450929 none CC1C(NC(=O)C(F)N2C=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 92, 92, 92, 194, 194, 201, 201, 201, 201, 71, 71, 71, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 92, 194, 201, 201, 201, 71, 71, 71, 71, 71, 71, 29, 29, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 782 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450929 none CC1C(NC(=O)C(F)N2C=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 10, 17, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 16, 39, 39, 39, 1, 1, 1, 1, 1, 1, 10, 10, 71] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450929 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450929 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450929/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450929 Building REAL300024450930 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450930' /scratch/stefan/7786230/working/building/REAL300024450930 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450930 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450930/0 /scratch/stefan/7786230/working/building/REAL300024450930 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/835 `/scratch/stefan/7786230/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450930/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450930 none CC1C(NC(=O)CC2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 31, 31, 5, 31, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 55, 55, 93, 135, 201, 201, 201, 201, 201, 41, 41, 41, 41, 41, 31, 5, 5, 1, 1, 41, 41, 41, 41, 41, 41, 93, 93, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 535 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: REAL300024450930 none CC1C(NC(=O)CC2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 84, 84, 84, 198, 201, 201, 201, 201, 69, 69, 69, 66, 28, 66, 12, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 84, 198, 198, 201, 201, 69, 69, 69, 69, 69, 69, 28, 28, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 748 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450930 none CC1C(NC(=O)CC2=CN=CO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 1, 1, 8, 1, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 21, 41, 41, 41, 41, 1, 1, 1, 1, 1, 3, 3, 10, 17, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 4, 21, 21, 41, 41, 1, 1, 1, 1, 1, 1, 10, 10, 69] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450930 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450930 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450930/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450930 Building REAL300024450931 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450931' /scratch/stefan/7786230/working/building/REAL300024450931 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450931 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450931/0 /scratch/stefan/7786230/working/building/REAL300024450931 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/836 `/scratch/stefan/7786230/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450931/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450931 none CC1C(NC(=O)C[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 52, 52, 89, 133, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 89, 89, 201] 201 rigid atoms, others: [43, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 548 number of broken/clashed sets: 10 ./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: REAL300024450931 none CC1C(NC(=O)C[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 55, 55, 63, 63, 63, 171, 201, 201, 201, 201, 201, 201, 55, 55, 55, 52, 25, 52, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 63, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 55, 55, 25, 25, 1] 201 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 739 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450931 none CC1C(NC(=O)C[C@@H]2CC=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 20, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 3, 16, 16, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 55] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450931 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450931 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450931/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450931 Building REAL300024450932 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450932' /scratch/stefan/7786230/working/building/REAL300024450932 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450932 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450932/0 /scratch/stefan/7786230/working/building/REAL300024450932 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/837 `/scratch/stefan/7786230/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C[NH+]2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450932/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450932 none CC1C(NC(=O)C[NH+]2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 25, 29, 33, 33, 33, 33, 33, 16, 16, 16, 16, 16, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 25, 25, 33] 33 rigid atoms, others: [43, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 25 ./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: REAL300024450932 none CC1C(NC(=O)C[NH+]2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 23, 23, 23, 23, 31, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 17, 23, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 31, 31, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 17, 17, 1] 33 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 115 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450932 none CC1C(NC(=O)C[NH+]2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 10, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 2, 2, 4, 7, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 3, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 4, 4, 23] 33 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450932 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450932/1 /scratch/stefan/7786230/working/building/REAL300024450932 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/838 `/scratch/stefan/7786230/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450932.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450932/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450932 none CC1C(NC(=O)CN2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 36, 36, 77, 119, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 77, 77, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 520 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: REAL300024450932 none CC1C(NC(=O)CN2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 136, 136, 136, 201, 201, 201, 201, 201, 201, 98, 98, 98, 95, 31, 95, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 31, 31, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 776 number of broken/clashed sets: 4 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450932 none CC1C(NC(=O)CN2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 3, 11, 22, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 6, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 11, 11, 98] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450932 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450932 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450932/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450932/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450932 Building REAL300024450933 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450933' /scratch/stefan/7786230/working/building/REAL300024450933 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450933 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450933/0 /scratch/stefan/7786230/working/building/REAL300024450933 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/839 `/scratch/stefan/7786230/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450933/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450933 none CC1C(NC(=O)CC2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 50, 50, 85, 122, 201, 201, 201, 201, 201, 33, 33, 33, 33, 33, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 85, 85, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 536 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: REAL300024450933 none CC1C(NC(=O)CC2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 76, 76, 76, 185, 201, 201, 201, 201, 201, 62, 62, 62, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 76, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 29, 29, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 766 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450933 none CC1C(NC(=O)CC2CC3CC3C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 3, 3, 9, 16, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 3, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 9, 9, 62] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450933 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450933 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450933/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450933 Building REAL300024450934 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450934' /scratch/stefan/7786230/working/building/REAL300024450934 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450934 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450934/0 /scratch/stefan/7786230/working/building/REAL300024450934 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/840 `/scratch/stefan/7786230/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NOC(CF)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450934/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450934 none CC1C(NC(=O)C2=NOC(CF)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 12, 1, 5, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 1, 9, 9, 9, 9, 9, 12, 12, 35, 46, 87, 87, 87, 87, 87, 9, 9, 9, 9, 9, 5, 6, 6, 1, 9, 9, 9, 9, 9, 9, 35, 35, 87] 87 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 12] set([0, 1, 2, 3, 5, 11, 13, 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, 44]) total number of confs: 230 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: REAL300024450934 none CC1C(NC(=O)C2=NOC(CF)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 12, 1, 5, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [57, 57, 57, 57, 66, 66, 66, 87, 87, 87, 87, 87, 87, 57, 57, 57, 54, 38, 54, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 66, 87, 87, 87, 57, 57, 57, 57, 57, 57, 38, 38, 1] 87 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 255 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450934 none CC1C(NC(=O)C2=NOC(CF)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 12, 1, 5, 15, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 24, 9, 1, 1, 1, 1, 1, 3, 3, 10, 18, 57, 57, 57, 57, 57, 2, 2, 2, 1, 1, 4, 24, 24, 9, 1, 1, 1, 1, 1, 1, 10, 10, 57] 87 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450934 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450934 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450934/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450934 Building REAL300024450935 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450935' /scratch/stefan/7786230/working/building/REAL300024450935 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450935 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450935/0 /scratch/stefan/7786230/working/building/REAL300024450935 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/841 `/scratch/stefan/7786230/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450935/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450935 none CC1C(NC(=O)C2=CC=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 35, 53, 83, 83, 83, 83, 83, 8, 8, 8, 8, 8, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 35, 35, 83] 83 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 217 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: REAL300024450935 none CC1C(NC(=O)C2=CC=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 80, 80, 80, 83, 83, 83, 83, 83, 83, 65, 65, 65, 62, 38, 62, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 80, 83, 83, 83, 65, 65, 65, 65, 65, 65, 38, 38, 1] 83 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 275 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450935 none CC1C(NC(=O)C2=CC=CC(F)=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 15, 28, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 4, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 15, 65] 83 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450935 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450935 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450935/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450935 Building REAL300024450936 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450936' /scratch/stefan/7786230/working/building/REAL300024450936 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450936 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450936/0 /scratch/stefan/7786230/working/building/REAL300024450936 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/842 `/scratch/stefan/7786230/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450936/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450936 none COC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 123, 201, 201, 123, 123, 66, 66, 66, 66, 66, 64, 45, 64, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 66, 66, 66, 66, 66, 66, 66, 45, 45, 1, 66, 66, 66, 66] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 843 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450936 none COC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 19, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 66, 66, 66, 66, 66, 1, 1, 24, 24, 24, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 66, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450936 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450936 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450936/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450936 Building REAL300024450937 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450937' /scratch/stefan/7786230/working/building/REAL300024450937 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450937 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450937/0 /scratch/stefan/7786230/working/building/REAL300024450937 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/843 `/scratch/stefan/7786230/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C) `REAL300024450937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450937/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450937 none CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [199, 199, 184, 114, 114, 114, 80, 80, 80, 80, 80, 79, 37, 79, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 184, 193, 193, 193, 199, 199, 199, 199, 199, 199, 199, 184, 114, 80, 80, 80, 80, 80, 80, 80, 37, 37, 1, 80, 80, 80, 80, 193, 193, 193, 193, 193, 193] 199 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 891 number of broken/clashed sets: 123 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450937 none CCCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 25, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 80, 80, 80, 80, 80, 1, 1, 12, 19, 18, 19, 29, 29, 29, 29, 29, 26, 26, 12, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 80, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19] 199 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 12, 47, 43, 40, 22, 41, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 298 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450937 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450937 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450937/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450937 Building REAL300024450938 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450938' /scratch/stefan/7786230/working/building/REAL300024450938 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450938 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450938/0 /scratch/stefan/7786230/working/building/REAL300024450938 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/844 `/scratch/stefan/7786230/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450938/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450938 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 35, 84, 84, 84, 84, 84, 1, 1, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 84, 1, 2, 2, 2] 105 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 179 number of broken/clashed sets: 23 ./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: REAL300024450938 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 100, 100, 100, 84, 84, 84, 84, 84, 75, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 105, 105, 105, 105, 105, 105, 100, 84, 84, 84, 84, 84, 84, 84, 38, 38, 1, 84, 84, 84, 84] 105 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 335 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450938 none CC1=CN=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 11, 11, 37, 62, 105, 105, 105, 105, 105, 7, 7, 1, 2, 2, 2, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 37, 37, 105, 7, 7, 7, 7] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 264 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450938 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450938 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450938/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450938 Building REAL300024450939 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450939' /scratch/stefan/7786230/working/building/REAL300024450939 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450939 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450939/0 /scratch/stefan/7786230/working/building/REAL300024450939 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/845 `/scratch/stefan/7786230/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450939/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450939 none CC1C(NC(=O)C(C)(C)[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 36, 36, 36, 74, 74, 74, 145, 145, 145, 146, 143, 138, 36, 36, 36, 36, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 74, 145, 145, 145, 145, 145, 145, 146, 146, 146, 146, 146, 146, 36, 36, 36, 36, 36, 36, 27, 27, 1] 146 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 642 number of broken/clashed sets: 146 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450939 none CC1C(NC(=O)C(C)(C)[NH+](C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 31, 31, 31, 36, 33, 34, 1, 1, 1, 1, 1, 3, 3, 8, 12, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 6, 31, 31, 31, 31, 31, 31, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 8, 8, 36] 146 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 13, 14, 45, 16, 49, 50, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 237 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450939 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450939 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450939/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450939 Building REAL300024450940 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450940' /scratch/stefan/7786230/working/building/REAL300024450940 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450940 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450940/0 /scratch/stefan/7786230/working/building/REAL300024450940 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/846 `/scratch/stefan/7786230/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)(F)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450940/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450940 none CC1C(NC(=O)C(F)(F)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 15, 15, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 12, 2, 2, 2, 2, 2, 2, 2, 2, 1] 12 rigid atoms, others: [42, 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]) total number of confs: 25 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450940 none CC1C(NC(=O)C(F)(F)CO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 15, 15, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 4, 4, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2] 12 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450940 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450940 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450940/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450940 Building REAL300024450941 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450941' /scratch/stefan/7786230/working/building/REAL300024450941 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450941 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450941/0 /scratch/stefan/7786230/working/building/REAL300024450941 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/847 `/scratch/stefan/7786230/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450941/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450941 none CC1C(NC(=O)CCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 36, 36, 36, 41, 41, 41, 157, 187, 201, 201, 36, 36, 36, 35, 24, 35, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 41, 157, 157, 201, 201, 201, 201, 201, 201, 603, 36, 36, 36, 36, 36, 36, 24, 24, 1] 603 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47]) total number of confs: 1516 number of broken/clashed sets: 120 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450941 none CC1C(NC(=O)CCCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 13, 18, 21, 39, 1, 1, 1, 1, 1, 3, 3, 6, 10, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 3, 13, 13, 21, 21, 21, 21, 39, 39, 117, 1, 1, 1, 1, 1, 1, 6, 6, 36] 603 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 11, 12, 13, 14, 44, 43, 45, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 382 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450941 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450941 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450941/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450941 Building REAL300024450942 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450942' /scratch/stefan/7786230/working/building/REAL300024450942 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450942 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450942/0 /scratch/stefan/7786230/working/building/REAL300024450942 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/848 `/scratch/stefan/7786230/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1) `REAL300024450942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450942/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450942 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 28, 97, 97, 97, 97, 97, 1, 1, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 97, 1, 2, 2, 2, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 179 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: REAL300024450942 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 135, 135, 135, 97, 97, 97, 97, 97, 95, 50, 95, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 201, 201, 201, 135, 97, 97, 97, 97, 97, 97, 97, 50, 50, 1, 97, 97, 97, 97, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 547 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450942 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 12, 12, 12, 12, 12, 20, 20, 57, 109, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 12, 12, 12, 12, 57, 57, 201, 12, 12, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 475 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450942 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450942 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450942/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450942 Building REAL300024450943 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450943' /scratch/stefan/7786230/working/building/REAL300024450943 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450943 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450943/0 /scratch/stefan/7786230/working/building/REAL300024450943 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/849 `/scratch/stefan/7786230/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450943/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450943 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 32, 81, 81, 81, 81, 81, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 81, 1, 2, 2, 2, 9] 111 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 22 ./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: REAL300024450943 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 110, 110, 110, 81, 81, 81, 81, 81, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 111, 111, 111, 111, 111, 111, 110, 81, 81, 81, 81, 81, 81, 81, 39, 39, 1, 81, 81, 81, 81, 111] 111 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 358 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450943 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 15, 15, 43, 63, 111, 111, 111, 111, 111, 9, 9, 1, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 43, 43, 111, 9, 9, 9, 9, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 291 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450943 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450943 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450943/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450943 Building REAL300024450944 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450944' /scratch/stefan/7786230/working/building/REAL300024450944 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450944 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450944/0 /scratch/stefan/7786230/working/building/REAL300024450944 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/850 `/scratch/stefan/7786230/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450944/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450944 none CC1C(NC(=O)C2CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 20, 20, 52, 93, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 52, 52, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 438 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: REAL300024450944 none CC1C(NC(=O)C2CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [74, 74, 74, 74, 108, 108, 108, 201, 201, 201, 201, 201, 74, 74, 74, 71, 40, 71, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 108, 201, 201, 201, 201, 201, 201, 74, 74, 74, 74, 74, 74, 40, 40, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 637 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450944 none CC1C(NC(=O)C2CNC(=O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 11, 24, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 74] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450944 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450944 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450944/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450944 Building REAL300024450945 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450945' /scratch/stefan/7786230/working/building/REAL300024450945 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450945 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450945/0 /scratch/stefan/7786230/working/building/REAL300024450945 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/851 `/scratch/stefan/7786230/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450945/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450945 none CC1C(NC(=O)COC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 32, 32, 53, 53, 53, 173, 201, 201, 201, 201, 32, 32, 32, 32, 29, 32, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 53, 173, 173, 32, 32, 32, 32, 32, 32, 29, 29, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 718 number of broken/clashed sets: 82 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450945 none CC1C(NC(=O)COC(F)(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 25, 56, 73, 73, 73, 1, 1, 1, 1, 1, 3, 3, 6, 9, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 5, 25, 25, 1, 1, 1, 1, 1, 1, 6, 6, 32] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 272 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450945 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450945 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450945/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450945 Building REAL300024450946 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450946' /scratch/stefan/7786230/working/building/REAL300024450946 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450946 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450946/0 /scratch/stefan/7786230/working/building/REAL300024450946 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/852 `/scratch/stefan/7786230/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450946/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450946 none CC1C(NC(=O)[C@@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 56, 117, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 56, 56, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 450 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: REAL300024450946 none CC1C(NC(=O)[C@@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [135, 135, 135, 135, 191, 191, 191, 201, 201, 201, 201, 201, 201, 135, 135, 135, 130, 53, 130, 12, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 191, 201, 201, 201, 201, 135, 135, 135, 135, 135, 135, 53, 53, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 648 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450946 none CC1C(NC(=O)[C@@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 12, 41, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 6, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 135] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450946 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450946 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450946/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450946 Building REAL300024450947 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450947' /scratch/stefan/7786230/working/building/REAL300024450947 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450947 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450947/0 /scratch/stefan/7786230/working/building/REAL300024450947 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/853 `/scratch/stefan/7786230/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450947/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450947 none CC1C(NC(=O)C2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 22, 22, 56, 108, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 7, 1, 1, 14, 14, 14, 14, 14, 14, 56, 56, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 448 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: REAL300024450947 none CC1C(NC(=O)C2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [155, 155, 155, 155, 181, 181, 181, 201, 201, 201, 201, 155, 155, 155, 150, 67, 150, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 181, 201, 201, 155, 155, 155, 155, 155, 155, 67, 67, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 602 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450947 none CC1C(NC(=O)C2=CN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 12, 44, 155, 155, 155, 155, 155, 2, 2, 2, 1, 1, 6, 14, 14, 1, 1, 1, 1, 1, 1, 12, 12, 155] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450947 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450947 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450947/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450947 Building REAL300024450948 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450948' /scratch/stefan/7786230/working/building/REAL300024450948 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450948 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450948/0 /scratch/stefan/7786230/working/building/REAL300024450948 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/854 `/scratch/stefan/7786230/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1) `REAL300024450948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450948/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450948 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 82, 82, 82, 82, 82, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 82, 1, 2, 2, 2, 15] 111 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 176 number of broken/clashed sets: 24 ./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: REAL300024450948 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 101, 101, 101, 82, 82, 82, 82, 82, 75, 40, 75, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 111, 111, 111, 111, 111, 111, 101, 82, 82, 82, 82, 82, 82, 82, 40, 40, 1, 82, 82, 82, 82, 111] 111 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 365 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450948 none CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 21, 21, 48, 66, 111, 111, 111, 111, 111, 15, 15, 1, 2, 2, 2, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 48, 48, 111, 15, 15, 15, 15, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 29, 30] set([6, 7, 8, 9, 10, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450948 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450948 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450948/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450948 Building REAL300024450949 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450949' /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450949 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450949/0 /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/855 `/scratch/stefan/7786230/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450949/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4] 4 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 15 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: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 5 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4] 4 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450949/1 /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/856 `/scratch/stefan/7786230/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450949.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450949/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 16, 21, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 16, 16, 26] 26 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 8 ./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: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 16, 21, 10, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 16, 16, 1] 26 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 78 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCC[N@H+]2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 8, 13, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 21] 26 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450949/2 /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/857 `/scratch/stefan/7786230/working/3D/857' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450949.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450949/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 28, 51, 86, 86, 86, 86, 86, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 28, 28, 86] 86 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 208 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: REAL300024450949 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 86, 86, 86, 86, 86, 86, 71, 71, 71, 68, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 71, 71, 71, 71, 71, 71, 36, 36, 1] 86 rigid atoms, others: [20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 294 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450949 none CC1C(NC(=O)C2CCCCN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 16, 33, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 16, 16, 71] 86 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 13, 14, 45, 16, 49, 50, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53]) total number of confs: 156 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450949 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450949 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450949/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450949/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450949/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450949 Building REAL300024450950 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450950' /scratch/stefan/7786230/working/building/REAL300024450950 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450950 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450950/0 /scratch/stefan/7786230/working/building/REAL300024450950 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/858 `/scratch/stefan/7786230/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450950/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450950 none CC1C(NC(=O)C2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 7, 7, 1, 7, 1, 1, 7, 1, 1, 23, 23, 23, 23, 23, 35, 35, 80, 123, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 7, 7, 7, 21, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 80, 80, 201] 603 rigid atoms, others: [34, 35, 4, 37, 6, 7, 9, 10, 36] set([0, 1, 2, 3, 5, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 569 number of broken/clashed sets: 265 ./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: REAL300024450950 none CC1C(NC(=O)C2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 59, 59, 59, 113, 113, 113, 201, 201, 201, 201, 59, 59, 59, 56, 40, 56, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 113, 201, 201, 603, 201, 201, 201, 201, 59, 59, 59, 59, 59, 59, 40, 40, 1] 603 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 1260 number of broken/clashed sets: 265 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450950 none CC1C(NC(=O)C2(CO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 23, 43, 23, 23, 1, 1, 1, 1, 1, 3, 3, 9, 18, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 6, 43, 43, 129, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 9, 9, 59] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 265 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450950 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450950 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450950/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450950 Building REAL300024450951 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450951' /scratch/stefan/7786230/working/building/REAL300024450951 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450951 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450951/0 /scratch/stefan/7786230/working/building/REAL300024450951 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/859 `/scratch/stefan/7786230/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450951/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450951 none CCC1=CNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 104, 104, 104, 104, 104, 1, 1, 27, 27, 27, 27, 27, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 104, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 250 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: REAL300024450951 none CCC1=CNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 161, 161, 161, 161, 161, 135, 135, 135, 104, 104, 104, 104, 104, 97, 30, 97, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 201, 201, 161, 161, 161, 135, 104, 104, 104, 104, 104, 104, 104, 30, 30, 1, 104, 104, 104, 104] 201 rigid atoms, others: [45, 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, 43, 44, 46, 47, 48, 49]) total number of confs: 697 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450951 none CCC1=CNC=C1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 16, 16, 16, 16, 16, 24, 24, 54, 87, 161, 161, 161, 161, 161, 16, 16, 4, 4, 4, 4, 4, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 54, 54, 161, 16, 16, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34] set([0, 8, 9, 10, 11, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450951 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450951 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450951/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450951 Building REAL300024450952 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450952' /scratch/stefan/7786230/working/building/REAL300024450952 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450952 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450952/0 /scratch/stefan/7786230/working/building/REAL300024450952 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/860 `/scratch/stefan/7786230/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CCC[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450952/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450952 none CC1C(NC(=O)[C@@H]2CCC[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 38, 38, 78, 119, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 27, 78, 78, 201] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 544 number of broken/clashed sets: 72 ./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: REAL300024450952 none CC1C(NC(=O)[C@@H]2CCC[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 73, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 71, 52, 71, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 117, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 73, 52, 52, 1] 201 rigid atoms, others: [51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 641 number of broken/clashed sets: 72 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450952 none CC1C(NC(=O)[C@@H]2CCC[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 47, 1, 1, 1, 1, 1, 3, 3, 10, 20, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 6, 27, 27, 27, 27, 27, 27, 47, 47, 1, 1, 1, 1, 1, 1, 10, 10, 73] 201 rigid atoms, others: [0, 1, 2, 3, 48, 33, 32, 43, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450952 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450952 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450952/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450952 Building REAL300024450953 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450953' /scratch/stefan/7786230/working/building/REAL300024450953 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450953 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450953/0 /scratch/stefan/7786230/working/building/REAL300024450953 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/861 `/scratch/stefan/7786230/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450953/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450953 none CC(C)[C@@H](O)[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 201, 201, 201, 201, 137, 201, 201, 137, 137, 109, 109, 109, 109, 109, 95, 31, 95, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 137, 109, 109, 109, 109, 109, 109, 109, 31, 31, 1, 109, 109, 109, 109] 603 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 1342 number of broken/clashed sets: 100 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450953 none CC(C)[C@@H](O)[C@@H](C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 17, 20, 15, 17, 17, 4, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 34, 109, 109, 109, 109, 109, 1, 1, 20, 20, 20, 20, 20, 20, 20, 51, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 109, 1, 2, 2, 2] 603 rigid atoms, others: [45, 43, 47, 41, 42, 11, 12, 13, 14, 15, 16, 17, 51, 46, 27, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 311 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450953 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450953 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450953/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450953 Building REAL300024450954 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450954' /scratch/stefan/7786230/working/building/REAL300024450954 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450954 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450954/0 /scratch/stefan/7786230/working/building/REAL300024450954 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/862 `/scratch/stefan/7786230/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024450954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450954/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450954 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 30, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 103, 103, 103, 103, 103, 1, 1, 30, 30, 37, 37, 37, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 103, 1, 2, 2, 2, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 18 ./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: REAL300024450954 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 107, 107, 107, 103, 103, 103, 103, 103, 93, 28, 93, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 188, 188, 107, 103, 103, 103, 103, 103, 103, 103, 28, 28, 1, 103, 103, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 724 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450954 none COC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 6, 25, 25, 25, 30, 30, 30, 30, 30, 42, 42, 88, 129, 201, 201, 201, 201, 201, 30, 30, 1, 1, 5, 5, 5, 6, 6, 25, 30, 30, 30, 30, 30, 30, 30, 88, 88, 201, 30, 30, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 46, 47, 48, 49, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 550 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450954 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450954 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450954/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450954 Building REAL300024450955 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450955' /scratch/stefan/7786230/working/building/REAL300024450955 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450955 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450955/0 /scratch/stefan/7786230/working/building/REAL300024450955 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/863 `/scratch/stefan/7786230/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450955/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450955 none CC1C(NC(=O)CC2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 25, 25, 7, 25, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 47, 47, 81, 122, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 25, 7, 7, 2, 2, 2, 1, 32, 32, 32, 32, 32, 32, 81, 81, 201] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 536 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: REAL300024450955 none CC1C(NC(=O)CC2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 85, 85, 85, 179, 201, 201, 201, 201, 201, 70, 70, 70, 70, 27, 70, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 85, 179, 179, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 27, 27, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 705 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450955 none CC1C(NC(=O)CC2=NN(C)N=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 8, 8, 5, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 20, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 3, 18, 18, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 70] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450955 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450955 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450955/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450955 Building REAL300024450956 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450956' /scratch/stefan/7786230/working/building/REAL300024450956 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450956 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450956/0 /scratch/stefan/7786230/working/building/REAL300024450956 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/864 `/scratch/stefan/7786230/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450956/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450956 none CC1C(NC(=O)CC2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 31, 31, 5, 31, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 52, 52, 98, 137, 201, 201, 201, 201, 201, 44, 44, 44, 44, 44, 31, 5, 5, 1, 1, 1, 44, 44, 44, 44, 44, 44, 98, 98, 201] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 575 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: REAL300024450956 none CC1C(NC(=O)CC2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 61, 61, 61, 85, 85, 85, 172, 201, 201, 201, 201, 61, 61, 61, 61, 43, 61, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 85, 172, 172, 201, 201, 201, 61, 61, 61, 61, 61, 61, 43, 43, 1] 201 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 782 number of broken/clashed sets: 59 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450956 none CC1C(NC(=O)CC2CC2(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 22, 44, 44, 44, 44, 1, 1, 1, 1, 1, 3, 3, 9, 15, 61, 61, 61, 61, 61, 2, 2, 2, 1, 1, 4, 22, 22, 44, 44, 44, 1, 1, 1, 1, 1, 1, 9, 9, 61] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 250 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450956 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450956 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450956/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450956 Building REAL300024450957 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450957' /scratch/stefan/7786230/working/building/REAL300024450957 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450957 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450957/0 /scratch/stefan/7786230/working/building/REAL300024450957 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/865 `/scratch/stefan/7786230/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450957/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450957 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 43, 65, 109, 109, 109, 109, 109, 7, 7, 7, 7, 7, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 43, 43, 109] 109 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 24 ./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: REAL300024450957 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 102, 102, 102, 109, 109, 109, 109, 109, 109, 84, 84, 84, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 102, 109, 109, 109, 84, 84, 84, 84, 84, 84, 39, 39, 1] 109 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 344 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450957 none CC1C(NC(=O)C2=CC(=O)NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 11, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 4, 4, 18, 35, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 4, 7, 7, 7, 1, 1, 1, 1, 1, 1, 18, 18, 84] 109 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450957 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450957 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450957/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450957 Building REAL300024450958 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450958' /scratch/stefan/7786230/working/building/REAL300024450958 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450958 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450958/0 /scratch/stefan/7786230/working/building/REAL300024450958 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/866 `/scratch/stefan/7786230/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450958/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450958 none CC[C@H](C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 167, 201, 201, 109, 167, 167, 109, 109, 80, 80, 80, 80, 80, 74, 27, 74, 12, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 501, 109, 80, 80, 80, 80, 80, 80, 80, 27, 27, 1, 80, 80, 80, 80] 603 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1306 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450958 none CC[C@H](C)[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 27, 16, 27, 27, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 80, 80, 80, 80, 80, 1, 1, 32, 32, 32, 32, 32, 27, 27, 27, 48, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 80, 1, 2, 2, 2] 603 rigid atoms, others: [48, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 314 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450958 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450958 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450958/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450958 Building REAL300024450959 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450959' /scratch/stefan/7786230/working/building/REAL300024450959 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450959 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450959/0 /scratch/stefan/7786230/working/building/REAL300024450959 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/867 `/scratch/stefan/7786230/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@]23C[C@H]2[C@H](O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450959/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450959 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 49, 98, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 1, 1, 3, 1, 1, 10, 10, 10, 10, 10, 10, 49, 49, 201] 603 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 34 ./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: REAL300024450959 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 93, 93, 93, 99, 99, 99, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 92, 46, 92, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 99, 201, 201, 603, 201, 201, 93, 93, 93, 93, 93, 93, 46, 46, 1] 603 rigid atoms, others: [47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1060 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450959 none CC1C(NC(=O)[C@]23C[C@H]2[C@H](O)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 11, 28, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 3, 10, 10, 30, 10, 10, 1, 1, 1, 1, 1, 1, 11, 11, 93] 603 rigid atoms, others: [0, 1, 2, 3, 32, 40, 41, 42, 39, 44, 14, 15, 16, 17, 18, 43, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450959 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450959 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450959/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450959 Building REAL300024450960 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450960' /scratch/stefan/7786230/working/building/REAL300024450960 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450960 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450960/0 /scratch/stefan/7786230/working/building/REAL300024450960 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/868 `/scratch/stefan/7786230/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450960/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450960 none CCCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 192, 183, 173, 182, 75, 75, 75, 68, 68, 68, 68, 68, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 201, 201, 179, 177, 183, 183, 182, 182, 75, 68, 68, 68, 68, 68, 68, 68, 29, 29, 1, 68, 68, 68, 68] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 813 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450960 none CCCOCCCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 16, 13, 11, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 68, 68, 68, 68, 68, 1, 1, 41, 41, 41, 41, 41, 23, 23, 12, 12, 13, 13, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 68, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 303 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450960 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450960 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450960/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450960 Building REAL300024450961 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450961' /scratch/stefan/7786230/working/building/REAL300024450961 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450961 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450961/0 /scratch/stefan/7786230/working/building/REAL300024450961 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/869 `/scratch/stefan/7786230/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1) `REAL300024450961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450961/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450961 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 9, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 28, 69, 69, 69, 69, 69, 1, 1, 16, 16, 16, 16, 9, 16, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 69, 1, 2, 2, 2] 172 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 34 ./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: REAL300024450961 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 172, 168, 172, 172, 93, 93, 93, 69, 69, 69, 69, 69, 64, 38, 64, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 172, 172, 172, 172, 168, 172, 93, 69, 69, 69, 69, 69, 69, 69, 38, 38, 1, 69, 69, 69, 69] 172 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 475 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450961 none CC1=CC=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 24, 24, 69, 99, 172, 172, 172, 172, 172, 16, 16, 1, 2, 2, 2, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 69, 69, 172, 16, 16, 16, 16] 172 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 447 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450961 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450961 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450961/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450961 Building REAL300024450962 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450962' /scratch/stefan/7786230/working/building/REAL300024450962 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450962 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450962/0 /scratch/stefan/7786230/working/building/REAL300024450962 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/870 `/scratch/stefan/7786230/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450962/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450962 none CC1C(NC(=O)CCCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 38, 38, 43, 43, 43, 166, 190, 201, 190, 201, 38, 38, 38, 37, 24, 37, 13, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 43, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 38, 24, 24, 1] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 964 number of broken/clashed sets: 33 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450962 none CC1C(NC(=O)CCCCCF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 19, 23, 19, 43, 1, 1, 1, 1, 1, 3, 3, 6, 10, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 3, 14, 14, 23, 23, 23, 23, 23, 23, 40, 42, 1, 1, 1, 1, 1, 1, 6, 6, 38] 201 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 298 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450962 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450962 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450962/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450962 Building REAL300024450963 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450963' /scratch/stefan/7786230/working/building/REAL300024450963 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450963 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450963/0 /scratch/stefan/7786230/working/building/REAL300024450963 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/871 `/scratch/stefan/7786230/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3(CC3F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450963/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450963 none CC1C(NC(=O)C2CC3(CC3F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 34, 34, 85, 118, 187, 187, 187, 187, 187, 23, 23, 23, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 85, 85, 187] 187 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 526 number of broken/clashed sets: 31 ./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: REAL300024450963 none CC1C(NC(=O)C2CC3(CC3F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 71, 71, 89, 89, 89, 187, 187, 187, 187, 187, 187, 71, 71, 71, 68, 40, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 89, 187, 187, 187, 187, 187, 187, 187, 187, 71, 71, 71, 71, 71, 71, 40, 40, 1] 187 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 617 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450963 none CC1C(NC(=O)C2CC3(CC3F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 3, 13, 21, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 13, 13, 71] 187 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450963 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450963 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450963/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450963 Building REAL300024450964 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450964' /scratch/stefan/7786230/working/building/REAL300024450964 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450964 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450964/0 /scratch/stefan/7786230/working/building/REAL300024450964 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/872 `/scratch/stefan/7786230/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450964/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450964 none COC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6] 9 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] 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, 39, 40, 41, 42]) total number of confs: 30 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450964 none COC(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 7, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 1, 1, 8, 8, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 1, 2, 2, 2] 9 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450964 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450964 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450964/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450964 Building REAL300024450965 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450965' /scratch/stefan/7786230/working/building/REAL300024450965 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450965 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450965/0 /scratch/stefan/7786230/working/building/REAL300024450965 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/873 `/scratch/stefan/7786230/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1) `REAL300024450965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450965/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450965 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 28, 124, 124, 124, 124, 124, 1, 1, 12, 12, 12, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 124, 1, 2, 2, 2, 12] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 268 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: REAL300024450965 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 172, 172, 165, 165, 165, 124, 124, 124, 124, 124, 116, 31, 116, 13, 1, 1, 1, 1, 1, 1, 1, 124, 124, 172, 172, 172, 201, 201, 201, 201, 201, 165, 124, 124, 124, 124, 124, 124, 124, 31, 31, 1, 124, 124, 124, 124, 172] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47]) total number of confs: 684 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450965 none CCC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 12, 12, 12, 12, 18, 18, 49, 80, 172, 172, 172, 172, 172, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 4, 12, 12, 12, 12, 12, 12, 12, 49, 49, 172, 12, 12, 12, 12, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 387 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450965 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450965 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450965/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450965 Building REAL300024450966 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450966' /scratch/stefan/7786230/working/building/REAL300024450966 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450966 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450966/0 /scratch/stefan/7786230/working/building/REAL300024450966 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/874 `/scratch/stefan/7786230/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450966/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450966 none CC1C(NC(=O)COC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 37, 35, 35, 12, 34, 4, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 47, 47, 92, 139, 201, 201, 201, 201, 201, 37, 37, 37, 37, 37, 35, 12, 12, 1, 1, 37, 37, 37, 37, 37, 37, 92, 92, 201] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 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, 44, 45]) total number of confs: 552 number of broken/clashed sets: 10 ./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: REAL300024450966 none CC1C(NC(=O)COC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 84, 84, 84, 86, 86, 86, 160, 201, 201, 201, 201, 201, 84, 84, 84, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 86, 160, 160, 201, 201, 84, 84, 84, 84, 84, 84, 29, 29, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 658 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450966 none CC1C(NC(=O)COC2=NOC=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 12, 1, 8, 12, 1, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 31, 37, 37, 37, 37, 1, 1, 1, 1, 1, 3, 3, 11, 21, 84, 84, 84, 84, 84, 2, 2, 2, 1, 1, 3, 13, 13, 37, 37, 1, 1, 1, 1, 1, 1, 11, 11, 84] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 217 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450966 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450966 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450966/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450966 Building REAL300024450967 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450967' /scratch/stefan/7786230/working/building/REAL300024450967 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450967 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450967/0 /scratch/stefan/7786230/working/building/REAL300024450967 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/875 `/scratch/stefan/7786230/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C) `REAL300024450967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450967/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450967 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 89, 89, 89, 89, 89, 1, 1, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 89, 1, 2, 2, 2, 18, 18, 18] 180 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 35 ./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: REAL300024450967 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [180, 180, 180, 180, 123, 123, 123, 89, 89, 89, 89, 89, 82, 39, 82, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 180, 180, 180, 180, 180, 180, 123, 89, 89, 89, 89, 89, 89, 89, 39, 39, 1, 89, 89, 89, 89, 180, 180, 180] 180 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 515 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450967 none CC1=COC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 7, 7, 7, 18, 18, 18, 18, 18, 27, 27, 76, 110, 180, 180, 180, 180, 180, 18, 18, 1, 1, 2, 2, 2, 1, 7, 18, 18, 18, 18, 18, 18, 18, 76, 76, 180, 18, 18, 18, 18, 2, 2, 2] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 483 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450967 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450967 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450967/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450967 Building REAL300024450968 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450968' /scratch/stefan/7786230/working/building/REAL300024450968 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450968 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450968/0 /scratch/stefan/7786230/working/building/REAL300024450968 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/876 `/scratch/stefan/7786230/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450968/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450968 none CC1C(NC(=O)CC2=CN=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 22, 22, 7, 22, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 42, 42, 87, 123, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 22, 7, 7, 1, 1, 1, 29, 29, 29, 29, 29, 29, 87, 87, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 539 number of broken/clashed sets: 8 ./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: REAL300024450968 none CC1C(NC(=O)CC2=CN=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 85, 85, 85, 114, 114, 114, 197, 201, 201, 201, 201, 201, 85, 85, 85, 80, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 114, 197, 197, 201, 201, 201, 85, 85, 85, 85, 85, 85, 29, 29, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 771 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450968 none CC1C(NC(=O)CC2=CN=CC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 18, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 10, 17, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 5, 18, 18, 29, 29, 29, 1, 1, 1, 1, 1, 1, 10, 10, 85] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450968 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450968 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450968/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450968 Building REAL300024450969 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450969' /scratch/stefan/7786230/working/building/REAL300024450969 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450969 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450969/0 /scratch/stefan/7786230/working/building/REAL300024450969 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/877 `/scratch/stefan/7786230/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450969/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450969 none CCC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 25, 80, 80, 80, 80, 80, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 80, 1, 2, 2, 2] 89 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 49, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 24 ./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: REAL300024450969 none CCC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 85, 85, 85, 80, 80, 80, 80, 80, 77, 40, 77, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 85, 80, 80, 80, 80, 80, 80, 80, 40, 40, 1, 80, 80, 80, 80] 89 rigid atoms, others: [48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450969 none CCC1OCCC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 10, 10, 32, 48, 89, 89, 89, 89, 89, 7, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 32, 32, 89, 7, 7, 7, 7] 89 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 225 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450969 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450969 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450969/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450969 Building REAL300024450970 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450970' /scratch/stefan/7786230/working/building/REAL300024450970 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450970 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450970/0 /scratch/stefan/7786230/working/building/REAL300024450970 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/878 `/scratch/stefan/7786230/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC2CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450970/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450970 none CC1C(NC(=O)C23CC2CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 47, 98, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 47, 47, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 421 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: REAL300024450970 none CC1C(NC(=O)C23CC2CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 106, 106, 106, 112, 112, 112, 201, 201, 201, 201, 106, 106, 106, 105, 53, 105, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 112, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 106, 53, 53, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 517 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450970 none CC1C(NC(=O)C23CC2CC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 27, 106, 106, 106, 106, 106, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 106] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450970 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450970 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450970/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450970 Building REAL300024450971 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450971' /scratch/stefan/7786230/working/building/REAL300024450971 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450971 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450971/0 /scratch/stefan/7786230/working/building/REAL300024450971 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/879 `/scratch/stefan/7786230/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450971/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450971 none CCCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 125, 125, 125, 83, 83, 83, 67, 67, 67, 67, 67, 64, 27, 64, 12, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 83, 67, 67, 67, 67, 67, 67, 67, 27, 27, 1, 67, 67, 67, 67] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 876 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450971 none CCCC(C)=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 67, 67, 67, 67, 67, 1, 1, 30, 30, 30, 30, 30, 23, 23, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 67, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 241 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450971 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450971 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450971/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450971 Building REAL300024450972 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450972' /scratch/stefan/7786230/working/building/REAL300024450972 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450972 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450972/0 /scratch/stefan/7786230/working/building/REAL300024450972 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/880 `/scratch/stefan/7786230/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450972/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450972 none C=C[C@H](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 201, 201, 75, 75, 75, 57, 57, 57, 57, 57, 53, 23, 53, 11, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 201, 193, 193, 75, 57, 57, 57, 57, 57, 57, 57, 23, 23, 1, 57, 57, 57, 57] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 758 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450972 none C=C[C@H](C)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 25, 15, 25, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 57, 57, 57, 57, 57, 1, 1, 26, 26, 26, 25, 25, 25, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 57, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450972 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450972 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450972/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450972 Building REAL300024450973 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450973' /scratch/stefan/7786230/working/building/REAL300024450973 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450973 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450973/0 /scratch/stefan/7786230/working/building/REAL300024450973 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/881 `/scratch/stefan/7786230/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450973/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450973 none CC1C(NC(=O)C=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 32, 32, 7, 32, 7, 1, 1, 1, 1, 45, 45, 45, 45, 45, 54, 54, 104, 142, 201, 201, 201, 201, 201, 45, 45, 45, 45, 45, 32, 7, 7, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 104, 104, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 576 number of broken/clashed sets: 28 ./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: REAL300024450973 none CC1C(NC(=O)C=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 102, 102, 102, 177, 177, 201, 201, 80, 80, 80, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 102, 177, 177, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 80, 40, 40, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 691 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450973 none CC1C(NC(=O)C=CC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 15, 15, 45, 45, 1, 1, 1, 1, 1, 3, 3, 10, 18, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 15, 15, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 10, 10, 80] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450973 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450973 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450973/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450973 Building REAL300024450974 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450974' /scratch/stefan/7786230/working/building/REAL300024450974 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450974 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450974/0 /scratch/stefan/7786230/working/building/REAL300024450974 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/882 `/scratch/stefan/7786230/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CCC(CC2)O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450974/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450974 none CC1C(NC(=O)C23CCC(CC2)O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 59, 115, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 59, 59, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 454 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: REAL300024450974 none CC1C(NC(=O)C23CCC(CC2)O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 104, 104, 104, 124, 124, 124, 201, 201, 201, 201, 201, 201, 104, 104, 104, 103, 47, 103, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 104, 47, 47, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 529 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450974 none CC1C(NC(=O)C23CCC(CC2)O3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 11, 34, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 104] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450974 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450974 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450974/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450974 Building REAL300024450975 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450975' /scratch/stefan/7786230/working/building/REAL300024450975 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450975 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450975/0 /scratch/stefan/7786230/working/building/REAL300024450975 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/883 `/scratch/stefan/7786230/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450975/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450975 none CC=C(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 168, 101, 168, 201, 101, 101, 61, 61, 61, 61, 61, 58, 48, 58, 13, 1, 1, 1, 1, 1, 1, 1, 61, 61, 168, 168, 168, 168, 201, 201, 201, 201, 201, 101, 61, 61, 61, 61, 61, 61, 61, 48, 48, 1, 61, 61, 61, 61] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 755 number of broken/clashed sets: 77 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450975 none CC=C(CC)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 6, 31, 46, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 61, 61, 61, 61, 61, 1, 1, 31, 31, 31, 31, 46, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 268 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450975 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450975 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450975/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450975 Building REAL300024450976 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450976' /scratch/stefan/7786230/working/building/REAL300024450976 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450976 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450976/0 /scratch/stefan/7786230/working/building/REAL300024450976 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/884 `/scratch/stefan/7786230/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1) `REAL300024450976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450976/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450976 none CC1=C(F)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 32, 76, 76, 76, 76, 76, 1, 1, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 76, 1, 2, 2, 2, 8] 107 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 163 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: REAL300024450976 none CC1=C(F)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 94, 94, 94, 76, 76, 76, 76, 76, 70, 38, 70, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 107, 107, 107, 107, 107, 94, 76, 76, 76, 76, 76, 76, 76, 38, 38, 1, 76, 76, 76, 76, 107] 107 rigid atoms, others: [40, 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, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450976 none CC1=C(F)C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 8, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 12, 12, 42, 65, 107, 107, 107, 107, 107, 8, 8, 1, 1, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 42, 42, 107, 8, 8, 8, 8, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 26] set([6, 7, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450976 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450976/1 /scratch/stefan/7786230/working/building/REAL300024450976 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/885 `/scratch/stefan/7786230/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1F) `REAL300024450976.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450976/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450976 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 30, 72, 72, 72, 72, 72, 1, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 72, 1, 2, 2, 2] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 22 ./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: REAL300024450976 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 97, 97, 97, 97, 97, 97, 72, 72, 72, 72, 72, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 97, 97, 97, 97, 97, 97, 97, 72, 72, 72, 72, 72, 72, 72, 36, 36, 1, 72, 72, 72, 72] 97 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 321 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450976 none CC1=NNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 12, 12, 37, 54, 97, 97, 97, 97, 97, 8, 8, 1, 1, 2, 2, 2, 1, 5, 8, 8, 8, 8, 8, 8, 8, 37, 37, 97, 8, 8, 8, 8] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450976 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450976 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450976/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450976/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450976 Building REAL300024450977 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450977' /scratch/stefan/7786230/working/building/REAL300024450977 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450977 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450977/0 /scratch/stefan/7786230/working/building/REAL300024450977 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/886 `/scratch/stefan/7786230/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC23CC(C2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450977/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450977 none CC1C(NC(=O)CC23CC(C2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 25, 25, 7, 25, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 42, 42, 99, 142, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 99, 99, 201] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 563 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: REAL300024450977 none CC1C(NC(=O)CC23CC(C2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 110, 110, 110, 113, 113, 113, 201, 201, 201, 201, 201, 110, 110, 110, 95, 30, 95, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 110, 30, 30, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 735 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450977 none CC1C(NC(=O)CC23CC(C2)C3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 12, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 12, 23, 110, 110, 110, 110, 110, 2, 2, 2, 1, 1, 3, 12, 12, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 12, 12, 110] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450977 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450977 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450977/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450977 Building REAL300024450978 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450978' /scratch/stefan/7786230/working/building/REAL300024450978 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450978 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450978/0 /scratch/stefan/7786230/working/building/REAL300024450978 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/887 `/scratch/stefan/7786230/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(CC#C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450978/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450978 none C#CCC(CC#C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 191, 170, 91, 170, 191, 191, 91, 91, 71, 71, 71, 71, 71, 71, 36, 71, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 191, 191, 191, 170, 191, 191, 191, 91, 71, 71, 71, 71, 71, 71, 71, 36, 36, 1, 71, 71, 71, 71] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 957 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450978 none C#CCC(CC#C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 21, 11, 3, 11, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 15, 71, 71, 71, 71, 71, 1, 1, 21, 21, 21, 11, 21, 21, 21, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 1, 2, 2, 2] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450978 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450978 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450978/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450978 Building REAL300024450979 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450979' /scratch/stefan/7786230/working/building/REAL300024450979 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450979 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450979/0 /scratch/stefan/7786230/working/building/REAL300024450979 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/888 `/scratch/stefan/7786230/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)O) `REAL300024450979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450979/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450979 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7] 1 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12] 12 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 17 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450979 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7] 1 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 12] 12 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450979 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450979 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450979/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450979 Building REAL300024450980 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450980' /scratch/stefan/7786230/working/building/REAL300024450980 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450980 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450980/0 /scratch/stefan/7786230/working/building/REAL300024450980 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/889 `/scratch/stefan/7786230/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450980/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450980 none CCC(NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [159, 155, 88, 155, 170, 170, 170, 88, 88, 87, 87, 87, 87, 87, 81, 28, 81, 12, 1, 1, 1, 1, 1, 1, 1, 87, 87, 170, 170, 170, 170, 170, 155, 170, 170, 170, 88, 87, 87, 87, 87, 87, 87, 87, 28, 28, 1, 87, 87, 87, 87] 170 rigid atoms, others: [46, 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, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 787 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450980 none CCC(NC(N)=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 3, 11, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 24, 87, 87, 87, 87, 87, 1, 1, 15, 15, 15, 15, 15, 11, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 1, 2, 2, 2] 170 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450980 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450980 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450980/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450980 Building REAL300024450981 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450981' /scratch/stefan/7786230/working/building/REAL300024450981 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450981 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450981/0 /scratch/stefan/7786230/working/building/REAL300024450981 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/890 `/scratch/stefan/7786230/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450981/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450981 none CC1C(NC(=O)C2=COC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 1, 7, 7, 7, 7, 7, 11, 11, 37, 77, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 5, 1, 7, 7, 21, 1, 7, 7, 7, 7, 7, 7, 37, 37, 201] 603 rigid atoms, others: [33, 4, 37, 6, 7, 8, 9, 10, 12] set([0, 1, 2, 3, 5, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 416 number of broken/clashed sets: 51 ./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: REAL300024450981 none CC1C(NC(=O)C2=COC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 102, 102, 102, 106, 106, 106, 201, 201, 201, 201, 201, 201, 102, 102, 102, 100, 53, 100, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 106, 201, 201, 201, 603, 201, 102, 102, 102, 102, 102, 102, 53, 53, 1] 603 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1080 number of broken/clashed sets: 51 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450981 none CC1C(NC(=O)C2=COC(CO)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 5, 12, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 22, 7, 1, 1, 1, 1, 1, 3, 3, 12, 29, 102, 102, 102, 102, 102, 2, 2, 2, 1, 1, 3, 7, 22, 22, 66, 7, 1, 1, 1, 1, 1, 1, 12, 12, 102] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 305 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450981 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450981 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450981/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450981 Building REAL300024450982 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450982' /scratch/stefan/7786230/working/building/REAL300024450982 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450982 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450982/0 /scratch/stefan/7786230/working/building/REAL300024450982 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/891 `/scratch/stefan/7786230/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450982/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450982 none C=CC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3] 9 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 13 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450982 none C=CC(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 6, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2] 9 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450982 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450982 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450982/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450982 Building REAL300024450983 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450983' /scratch/stefan/7786230/working/building/REAL300024450983 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450983 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450983/0 /scratch/stefan/7786230/working/building/REAL300024450983 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/892 `/scratch/stefan/7786230/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450983/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450983 none CC1C(NC(=O)CCC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 40, 36, 36, 9, 36, 7, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 59, 59, 102, 138, 201, 201, 201, 201, 201, 40, 40, 40, 40, 40, 36, 9, 9, 7, 7, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 102, 102, 201] 603 rigid atoms, others: [43, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 581 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: REAL300024450983 none CC1C(NC(=O)CCC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 51, 51, 51, 54, 54, 54, 154, 166, 201, 201, 201, 201, 51, 51, 51, 51, 31, 51, 13, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 54, 154, 154, 166, 166, 603, 201, 201, 201, 201, 201, 201, 51, 51, 51, 51, 51, 51, 31, 31, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1404 number of broken/clashed sets: 69 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450983 none CC1C(NC(=O)CCC2(O)CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 14, 18, 40, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 9, 17, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 3, 14, 14, 18, 18, 120, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 9, 9, 51] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 347 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450983 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450983 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450983/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450983 Building REAL300024450984 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450984' /scratch/stefan/7786230/working/building/REAL300024450984 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450984 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450984/0 /scratch/stefan/7786230/working/building/REAL300024450984 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/893 `/scratch/stefan/7786230/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450984/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450984 none CCC(C)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [198, 195, 125, 195, 195, 201, 125, 125, 74, 74, 74, 74, 74, 72, 52, 72, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 201, 201, 195, 195, 195, 201, 201, 603, 125, 74, 74, 74, 74, 74, 74, 74, 52, 52, 1, 74, 74, 74, 74] 603 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1482 number of broken/clashed sets: 248 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450984 none CCC(C)(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 16, 6, 16, 16, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 74, 74, 74, 74, 74, 1, 1, 22, 22, 22, 22, 22, 16, 16, 16, 33, 33, 99, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 74, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 412 number of broken/clashed sets: 248 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450984 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450984 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450984/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450984 Building REAL300024450985 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450985' /scratch/stefan/7786230/working/building/REAL300024450985 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024450985 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450985/0 /scratch/stefan/7786230/working/building/REAL300024450985 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/894 `/scratch/stefan/7786230/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2([NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450985/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450985 none CC1C(NC(=O)C2([NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [4, 6, 39, 40, 41, 42, 11, 12, 7] set([0, 1, 2, 3, 5, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 13 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: REAL300024450985 none CC1C(NC(=O)C2([NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1] 3 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 7 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450985 none CC1C(NC(=O)C2([NH+](C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 19 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450985 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450985/1 /scratch/stefan/7786230/working/building/REAL300024450985 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/895 `/scratch/stefan/7786230/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(N(C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450985.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450985/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450985 none CC1C(NC(=O)C2(N(C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 38, 7, 40, 41, 10, 11, 39] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 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, 48, 49, 50]) total number of confs: 9 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: REAL300024450985 none CC1C(NC(=O)C2(N(C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 2 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 3 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450985 none CC1C(NC(=O)C2(N(C)C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 44, 42, 43, 12, 13, 14, 15, 16, 46, 45, 47, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450985 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450985 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450985/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450985/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450985 Building REAL300024450986 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450986' /scratch/stefan/7786230/working/building/REAL300024450986 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450986 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450986/0 /scratch/stefan/7786230/working/building/REAL300024450986 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/896 `/scratch/stefan/7786230/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC[NH+]2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450986/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450986 none CC1C(NC(=O)CC[NH+]2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 22, 22, 8, 22, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 24, 24, 24, 24, 24, 22, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 25] 25 rigid atoms, others: [45, 43, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 41, 39, 42] 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, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 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: REAL300024450986 none CC1C(NC(=O)CC[NH+]2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 12, 12, 14, 14, 14, 20, 21, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 14, 20, 20, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 1] 25 rigid atoms, others: [54, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 83 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450986 none CC1C(NC(=O)CC[NH+]2CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 16, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 3, 12, 12, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 4, 4, 12] 25 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 18, 14, 15, 16, 17, 50, 51, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450986 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450986 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450986/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450986 Building REAL300024450987 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450987' /scratch/stefan/7786230/working/building/REAL300024450987 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450987 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450987/0 /scratch/stefan/7786230/working/building/REAL300024450987 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/897 `/scratch/stefan/7786230/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CCC2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450987/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450987 none CC1C(NC(=O)CCC2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 32, 32, 9, 32, 5, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 43, 43, 88, 129, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 32, 9, 9, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 88, 88, 201] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 570 number of broken/clashed sets: 40 ./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: REAL300024450987 none CC1C(NC(=O)CCC2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 41, 41, 41, 160, 186, 201, 201, 201, 201, 36, 36, 36, 34, 24, 34, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 41, 160, 160, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 36, 24, 24, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 850 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450987 none CC1C(NC(=O)CCC2CC2(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 15, 20, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 7, 11, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 3, 15, 15, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 7, 7, 36] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450987 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450987 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450987/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450987 Building REAL300024450988 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450988' /scratch/stefan/7786230/working/building/REAL300024450988 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450988 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450988/0 /scratch/stefan/7786230/working/building/REAL300024450988 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/898 `/scratch/stefan/7786230/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450988/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450988 none CC1C(NC(=O)C=CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 35, 35, 9, 35, 9, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 49, 49, 102, 137, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 102, 102, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 543 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: REAL300024450988 none CC1C(NC(=O)C=CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 56, 56, 56, 58, 58, 58, 147, 147, 201, 201, 201, 201, 56, 56, 56, 55, 32, 55, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 58, 147, 147, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 56, 56, 56, 32, 32, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 660 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450988 none CC1C(NC(=O)C=CC2CCCO2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 39, 39, 39, 39, 1, 1, 1, 1, 1, 3, 3, 11, 19, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 11, 11, 56] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450988 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450988 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450988/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450988 Building REAL300024450989 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450989' /scratch/stefan/7786230/working/building/REAL300024450989 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450989 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450989/0 /scratch/stefan/7786230/working/building/REAL300024450989 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/899 `/scratch/stefan/7786230/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C)(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450989/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450989 none CC1C(NC(=O)C23CC(C)(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 23, 23, 78, 114, 163, 163, 163, 163, 163, 16, 16, 16, 16, 16, 12, 1, 1, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 78, 78, 163] 163 rigid atoms, others: [33, 34, 4, 38, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 443 number of broken/clashed sets: 29 ./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: REAL300024450989 none CC1C(NC(=O)C23CC(C)(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 87, 87, 87, 91, 91, 91, 163, 163, 163, 163, 163, 163, 87, 87, 87, 79, 38, 79, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 91, 163, 163, 163, 163, 163, 163, 163, 163, 163, 87, 87, 87, 87, 87, 87, 38, 38, 1] 163 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 399 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450989 none CC1C(NC(=O)C23CC(C)(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 16, 34, 87, 87, 87, 87, 87, 2, 2, 2, 1, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 16, 16, 87] 163 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450989 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450989 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450989/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450989 Building REAL300024450990 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450990' /scratch/stefan/7786230/working/building/REAL300024450990 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450990 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450990/0 /scratch/stefan/7786230/working/building/REAL300024450990 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/900 `/scratch/stefan/7786230/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(O)CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1) `REAL300024450990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450990/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450990 none C#CC1(O)CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 28, 85, 85, 85, 85, 85, 1, 1, 16, 16, 48, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 85, 1, 2, 2, 2, 16, 16] 603 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 126 ./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: REAL300024450990 none C#CC1(O)CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 201, 201, 201, 88, 88, 88, 85, 85, 85, 85, 85, 78, 42, 78, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 603, 201, 201, 201, 88, 85, 85, 85, 85, 85, 85, 85, 42, 42, 1, 85, 85, 85, 85, 201, 201] 603 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 1228 number of broken/clashed sets: 126 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450990 none C#CC1(O)CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 16, 16, 24, 24, 80, 121, 201, 201, 201, 201, 201, 16, 16, 1, 1, 6, 1, 1, 1, 11, 16, 16, 16, 16, 16, 16, 16, 80, 80, 201, 16, 16, 16, 16, 1, 1] 603 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 48, 26, 27, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 523 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450990 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450990 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450990/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450990 Building REAL300024450991 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450991' /scratch/stefan/7786230/working/building/REAL300024450991 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450991 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450991/0 /scratch/stefan/7786230/working/building/REAL300024450991 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/901 `/scratch/stefan/7786230/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024450991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450991/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450991 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 53, 53, 53, 53, 53, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 53, 1, 2, 2, 2, 11] 81 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 18 ./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: REAL300024450991 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 81, 81, 81, 81, 59, 59, 59, 53, 53, 53, 53, 53, 50, 32, 50, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 81, 81, 81, 81, 81, 81, 81, 81, 59, 53, 53, 53, 53, 53, 53, 53, 32, 32, 1, 53, 53, 53, 53, 81] 81 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450991 none CC1=C(C)NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 17, 17, 40, 50, 81, 81, 81, 81, 81, 11, 11, 1, 2, 2, 2, 2, 2, 2, 1, 7, 11, 11, 11, 11, 11, 11, 11, 40, 40, 81, 11, 11, 11, 11, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 236 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450991 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450991 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450991/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450991 Building REAL300024450992 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450992' /scratch/stefan/7786230/working/building/REAL300024450992 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450992 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450992/0 /scratch/stefan/7786230/working/building/REAL300024450992 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/902 `/scratch/stefan/7786230/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450992/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450992 none CC1C(NC(=O)C2CC3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 21, 21, 70, 115, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 70, 70, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 491 number of broken/clashed sets: 42 ./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: REAL300024450992 none CC1C(NC(=O)C2CC3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 77, 77, 77, 201, 201, 201, 201, 201, 201, 76, 76, 76, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 40, 40, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 609 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450992 none CC1C(NC(=O)C2CC3CCCC32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 11, 22, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 11, 11, 76] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450992 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450992 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450992/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450992 Building REAL300024450993 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450993' /scratch/stefan/7786230/working/building/REAL300024450993 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450993 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450993/0 /scratch/stefan/7786230/working/building/REAL300024450993 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/903 `/scratch/stefan/7786230/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450993/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450993 none CC1C(NC(=O)C23CC(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 70, 132, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 70, 70, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 491 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: REAL300024450993 none CC1C(NC(=O)C23CC(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [151, 151, 151, 151, 163, 163, 163, 201, 201, 201, 201, 201, 151, 151, 151, 146, 56, 146, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 163, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 151, 56, 56, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 566 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450993 none CC1C(NC(=O)C23CC(C2)CO3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 12, 39, 151, 151, 151, 151, 151, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 151] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450993 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450993 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450993/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450993 Building REAL300024450994 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450994' /scratch/stefan/7786230/working/building/REAL300024450994 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450994 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450994/0 /scratch/stefan/7786230/working/building/REAL300024450994 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/904 `/scratch/stefan/7786230/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450994/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450994 none CC1C(NC(=O)CC2CCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 36, 24, 24, 5, 24, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 56, 56, 89, 132, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 24, 5, 5, 1, 1, 1, 1, 1, 1, 6, 1, 1, 36, 36, 36, 36, 36, 36, 89, 89, 201] 603 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 555 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: REAL300024450994 none CC1C(NC(=O)CC2CCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 60, 60, 60, 70, 70, 70, 184, 201, 201, 201, 201, 201, 60, 60, 60, 53, 24, 53, 11, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 70, 184, 184, 201, 201, 201, 201, 201, 201, 603, 201, 201, 60, 60, 60, 60, 60, 60, 24, 24, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1344 number of broken/clashed sets: 48 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450994 none CC1C(NC(=O)CC2CCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 19, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 10, 17, 60, 60, 60, 60, 60, 2, 2, 2, 1, 1, 3, 19, 19, 36, 36, 36, 36, 36, 36, 108, 36, 36, 1, 1, 1, 1, 1, 1, 10, 10, 60] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 332 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450994 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450994 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450994/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450994 Building REAL300024450995 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450995' /scratch/stefan/7786230/working/building/REAL300024450995 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450995 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450995/0 /scratch/stefan/7786230/working/building/REAL300024450995 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/905 `/scratch/stefan/7786230/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)O) `REAL300024450995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450995/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450995 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [139, 121, 139, 121, 121, 67, 67, 67, 67, 67, 66, 48, 66, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 139, 143, 138, 143, 139, 139, 139, 121, 67, 67, 67, 67, 67, 67, 67, 48, 48, 1, 67, 67, 67, 67, 143, 143, 143, 143, 143, 143, 429] 429 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 972 number of broken/clashed sets: 124 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450995 none C[C@@H](C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 67, 67, 67, 67, 67, 1, 1, 17, 19, 17, 19, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 57] 429 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 265 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450995 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450995 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450995/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450995 Building REAL300024450996 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450996' /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024450996 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450996/0 /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/906 `/scratch/stefan/7786230/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C2)C[N@@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450996/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 13, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 13, 13, 14] 14 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 54 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: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 11, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 11, 11, 1] 14 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 27 number of broken/clashed sets: 3 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 6, 8, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 12] 14 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024450996/1 /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/907 `/scratch/stefan/7786230/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C2)C[N@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450996.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024450996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450996/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 27, 27, 54, 75, 102, 102, 102, 102, 102, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 18, 18, 54, 54, 102] 102 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 312 number of broken/clashed sets: 31 ./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: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 75, 75, 75, 102, 102, 102, 102, 102, 102, 102, 50, 50, 50, 50, 33, 50, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 75, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 50, 50, 50, 50, 50, 50, 33, 33, 1] 102 rigid atoms, others: [52, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 308 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)C[N@H+]3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 8, 16, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 8, 8, 50] 102 rigid atoms, others: [0, 1, 2, 3, 48, 49, 32, 44, 45, 14, 15, 16, 17, 18, 46, 47, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024450996/2 /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/908 `/scratch/stefan/7786230/working/3D/908' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C2)CN3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450996.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024450996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450996/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)CN3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 56, 118, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 56, 56, 201] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 36, 38, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 458 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: REAL300024450996 none CC1C(NC(=O)C23CC(C2)CN3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [127, 127, 127, 127, 139, 139, 139, 201, 201, 201, 201, 201, 201, 127, 127, 127, 124, 54, 124, 13, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 127, 54, 54, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 538 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450996 none CC1C(NC(=O)C23CC(C2)CN3C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 14, 39, 127, 127, 127, 127, 127, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 14, 14, 127] 201 rigid atoms, others: [0, 1, 2, 3, 48, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450996 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450996 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450996/0.* 1: /scratch/stefan/7786230/working/building/REAL300024450996/1.* 2: /scratch/stefan/7786230/working/building/REAL300024450996/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450996 Building REAL300024450997 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450997' /scratch/stefan/7786230/working/building/REAL300024450997 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450997 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450997/0 /scratch/stefan/7786230/working/building/REAL300024450997 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/909 `/scratch/stefan/7786230/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450997/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450997 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 48, 48, 88, 129, 201, 201, 201, 201, 201, 36, 36, 36, 36, 36, 29, 5, 5, 1, 2, 2, 2, 36, 36, 36, 36, 36, 36, 88, 88, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47]) total number of confs: 548 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: REAL300024450997 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 76, 76, 76, 100, 100, 100, 190, 201, 201, 201, 201, 201, 76, 76, 76, 71, 27, 71, 11, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 100, 190, 190, 201, 201, 201, 201, 76, 76, 76, 76, 76, 76, 27, 27, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450997 none CC1C(NC(=O)CC2=CN=NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 20, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 3, 3, 10, 17, 76, 76, 76, 76, 76, 2, 2, 2, 1, 1, 3, 20, 20, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 10, 10, 76] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450997 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450997 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450997/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450997 Building REAL300024450998 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450998' /scratch/stefan/7786230/working/building/REAL300024450998 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450998 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450998/0 /scratch/stefan/7786230/working/building/REAL300024450998 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/910 `/scratch/stefan/7786230/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C23CC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024450998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450998/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450998 none CC1C(NC(=O)C23CC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 52, 103, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 52, 52, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 432 number of broken/clashed sets: 23 ./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: REAL300024450998 none CC1C(NC(=O)C23CC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 102, 102, 102, 201, 201, 201, 201, 201, 98, 98, 98, 96, 50, 96, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 102, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 50, 50, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 483 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450998 none CC1C(NC(=O)C23CC(C2)OC3)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 12, 28, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 98] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450998 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450998 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450998/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450998 Building REAL300024450999 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024450999' /scratch/stefan/7786230/working/building/REAL300024450999 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024450999 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024450999/0 /scratch/stefan/7786230/working/building/REAL300024450999 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/911 `/scratch/stefan/7786230/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024450999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024450999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024450999/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450999 none CC(O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 14, 20, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 100, 100, 100, 100, 100, 1, 1, 20, 20, 20, 20, 60, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 100, 1, 2, 2, 2] 603 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 285 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: REAL300024450999 none CC(O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 185, 201, 185, 185, 130, 130, 130, 100, 100, 100, 100, 100, 91, 30, 91, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 201, 201, 603, 185, 185, 185, 185, 130, 100, 100, 100, 100, 100, 100, 100, 30, 30, 1, 100, 100, 100, 100] 603 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 1297 number of broken/clashed sets: 49 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024450999 none CC(O)C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 22, 22, 59, 101, 185, 185, 185, 185, 185, 14, 14, 4, 4, 4, 3, 9, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 59, 59, 185, 14, 14, 14, 14] 603 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 31] set([0, 2, 7, 8, 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, 45, 46, 47, 48, 49]) total number of confs: 455 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024450999 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024450999 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024450999/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024450999 Building REAL300024451000 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451000' /scratch/stefan/7786230/working/building/REAL300024451000 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451000 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451000/0 /scratch/stefan/7786230/working/building/REAL300024451000 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/912 `/scratch/stefan/7786230/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12) `REAL300024451000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451000/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451000 none C[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 59, 59, 59, 59, 59, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 59, 1, 2, 2, 2, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 22 ./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: REAL300024451000 none C[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 59, 59, 59, 59, 59, 59, 59, 59, 59, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 59, 59, 59, 59, 59, 31, 31, 1, 59, 59, 59, 59, 201, 201] 201 rigid atoms, others: [43, 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, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 381 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451000 none C[C@@H]1C[C@@]2(C(=O)NC3CCCN(C(=O)CSC4=NNC(=O)[N-]4)C3C)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 11, 11, 11, 11, 11, 17, 17, 48, 94, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 48, 48, 201, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 441 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451000 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451000 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451000/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451000 Building REAL300024451001 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451001' /scratch/stefan/7786230/working/building/REAL300024451001 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451001 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451001/0 /scratch/stefan/7786230/working/building/REAL300024451001 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/913 `/scratch/stefan/7786230/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2COC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451001/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451001 none CC1C(NC(=O)C2COC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 32, 32, 75, 104, 164, 164, 164, 164, 164, 24, 24, 24, 24, 24, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 24, 24, 24, 24, 24, 24, 75, 75, 164] 164 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 43, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 468 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: REAL300024451001 none CC1C(NC(=O)C2COC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 86, 86, 86, 164, 164, 164, 164, 164, 164, 57, 57, 57, 54, 35, 54, 13, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 86, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 57, 57, 57, 57, 57, 57, 35, 35, 1] 164 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 516 number of broken/clashed sets: 30 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451001 none CC1C(NC(=O)C2COC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 3, 11, 19, 57, 57, 57, 57, 57, 2, 2, 2, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 11, 11, 57] 164 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451001 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451001 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451001/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451001 Building REAL300024451002 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451002' /scratch/stefan/7786230/working/building/REAL300024451002 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451002 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451002/0 /scratch/stefan/7786230/working/building/REAL300024451002 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/914 `/scratch/stefan/7786230/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451002/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451002 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 46, 46, 85, 123, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 22, 8, 8, 1, 1, 30, 30, 30, 30, 30, 30, 85, 85, 201] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 6 ./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: REAL300024451002 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [92, 92, 92, 92, 116, 116, 116, 195, 201, 201, 201, 201, 92, 92, 92, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 116, 195, 195, 201, 201, 92, 92, 92, 92, 92, 92, 30, 30, 1] 201 rigid atoms, others: [44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 754 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451002 none CC1C(NC(=O)CN2C=NC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 8, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 18, 30, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 10, 17, 92, 92, 92, 92, 92, 2, 2, 2, 1, 1, 4, 18, 18, 30, 30, 1, 1, 1, 1, 1, 1, 10, 10, 92] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451002 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451002 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451002/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451002 Building REAL300024451003 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451003' /scratch/stefan/7786230/working/building/REAL300024451003 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451003 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451003/0 /scratch/stefan/7786230/working/building/REAL300024451003 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/915 `/scratch/stefan/7786230/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451003/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451003 none CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 81, 81, 81, 134, 134, 180, 180, 180, 180, 79, 79, 79, 77, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 81, 134, 134, 180, 180, 180, 180, 180, 180, 79, 79, 79, 79, 79, 79, 38, 38, 1] 180 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 589 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451003 none CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 10, 10, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 12, 25, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 3, 10, 10, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 12, 12, 79] 180 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451003 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451003 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451003/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451003 Building REAL300024451004 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451004' /scratch/stefan/7786230/working/building/REAL300024451004 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451004 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451004/0 /scratch/stefan/7786230/working/building/REAL300024451004 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/916 `/scratch/stefan/7786230/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451004/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451004 none CC1C(NC(=O)C2=CC=CC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 47, 68, 116, 116, 116, 116, 116, 12, 12, 12, 12, 12, 6, 1, 1, 1, 12, 12, 12, 12, 12, 12, 47, 47, 116] 116 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 22 ./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: REAL300024451004 none CC1C(NC(=O)C2=CC=CC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 113, 113, 113, 116, 116, 116, 116, 116, 116, 79, 79, 79, 75, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 113, 116, 116, 116, 79, 79, 79, 79, 79, 79, 38, 38, 1] 116 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451004 none CC1C(NC(=O)C2=CC=CC(=O)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 11, 1, 1, 1, 1, 1, 3, 3, 16, 31, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 5, 12, 12, 12, 1, 1, 1, 1, 1, 1, 16, 16, 79] 116 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451004 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451004 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451004/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451004 Building REAL300024451005 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451005' /scratch/stefan/7786230/working/building/REAL300024451005 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451005 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451005/0 /scratch/stefan/7786230/working/building/REAL300024451005 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/917 `/scratch/stefan/7786230/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C#CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451005/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451005 none CC1C(NC(=O)C#CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 46, 104, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 46, 46, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 36, 38, 37, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 416 number of broken/clashed sets: 25 ./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: REAL300024451005 none CC1C(NC(=O)C#CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 151, 66, 151, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 159, 66, 66, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 621 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451005 none CC1C(NC(=O)C#CC2(C)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 16, 51, 159, 159, 159, 159, 159, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 16, 16, 159] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451005 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451005 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451005/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451005 Building REAL300024451006 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451006' /scratch/stefan/7786230/working/building/REAL300024451006 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451006 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451006/0 /scratch/stefan/7786230/working/building/REAL300024451006 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/918 `/scratch/stefan/7786230/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1) `REAL300024451006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451006/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451006 none C=CC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 30, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 71, 71, 71, 71, 71, 1, 1, 30, 30, 30, 31, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 71, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 225 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: REAL300024451006 none C=CC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 176, 94, 94, 94, 71, 71, 71, 71, 71, 69, 26, 69, 12, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 176, 176, 94, 71, 71, 71, 71, 71, 71, 71, 26, 26, 1, 71, 71, 71, 71, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 783 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451006 none C=CC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 18, 18, 18, 30, 30, 30, 30, 30, 45, 45, 87, 136, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 3, 3, 3, 6, 6, 18, 30, 30, 30, 30, 30, 30, 30, 87, 87, 201, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 548 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451006 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451006 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451006/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451006 Building REAL300024451007 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451007' /scratch/stefan/7786230/working/building/REAL300024451007 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451007 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451007/0 /scratch/stefan/7786230/working/building/REAL300024451007 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/919 `/scratch/stefan/7786230/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=CN=C1) `REAL300024451007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451007/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451007 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [139, 88, 88, 88, 80, 80, 80, 80, 80, 76, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 139, 201, 201, 201, 201, 139, 139, 139, 139, 88, 80, 80, 80, 80, 80, 80, 80, 30, 30, 1, 80, 80, 80, 80, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 642 number of broken/clashed sets: 23 ./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: REAL300024451007 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 22, 22, 22, 27, 27, 27, 27, 27, 36, 36, 82, 125, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 8, 22, 27, 27, 27, 27, 27, 27, 27, 82, 82, 201, 27, 27, 27, 27, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 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]) total number of confs: 524 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451007 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 80, 80, 80, 80, 80, 1, 1, 13, 27, 27, 27, 27, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 80, 1, 2, 2, 2, 27, 27, 27] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451007 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451007 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451007/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451007 Building REAL300024451008 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451008' /scratch/stefan/7786230/working/building/REAL300024451008 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451008 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451008/0 /scratch/stefan/7786230/working/building/REAL300024451008 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/920 `/scratch/stefan/7786230/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451008/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451008 none CC1C(NC(=O)C2=CC=CNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 45, 70, 120, 120, 120, 120, 120, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 45, 45, 120] 120 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 309 number of broken/clashed sets: 24 ./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: REAL300024451008 none CC1C(NC(=O)C2=CC=CNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 118, 118, 118, 120, 120, 120, 120, 120, 120, 89, 89, 89, 80, 40, 80, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 118, 120, 120, 120, 120, 89, 89, 89, 89, 89, 89, 40, 40, 1] 120 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 381 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451008 none CC1C(NC(=O)C2=CC=CNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 16, 34, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 5, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 89] 120 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451008 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451008 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451008/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451008 Building REAL300024451009 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451009' /scratch/stefan/7786230/working/building/REAL300024451009 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451009 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451009/0 /scratch/stefan/7786230/working/building/REAL300024451009 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/921 `/scratch/stefan/7786230/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451009/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451009 none CC1C(NC(=O)CSC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 14, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 12, 12, 12, 32, 45, 45, 45, 9, 9, 9, 9, 8, 9, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 12, 32, 32, 45, 9, 9, 9, 9, 9, 9, 8, 8, 1] 45 rigid atoms, others: [42, 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]) total number of confs: 142 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451009 none CC1C(NC(=O)CSC(F)F)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 14, 5, 15, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 14, 29, 32, 32, 1, 1, 1, 1, 1, 3, 3, 5, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 3, 14, 14, 32, 1, 1, 1, 1, 1, 1, 5, 5, 9] 45 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451009 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451009 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451009/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451009 Building REAL300024451010 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451010' /scratch/stefan/7786230/working/building/REAL300024451010 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451010 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451010/0 /scratch/stefan/7786230/working/building/REAL300024451010 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/922 `/scratch/stefan/7786230/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024451010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451010/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451010 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 62, 62, 62, 62, 62, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 62, 1, 2, 2, 2, 25, 25, 25, 25] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 13, 47, 40, 41, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 42 ./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: REAL300024451010 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 75, 75, 62, 62, 62, 62, 62, 57, 37, 57, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 62, 62, 62, 62, 62, 62, 62, 37, 37, 1, 62, 62, 62, 62, 201, 201, 201, 201] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 612 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451010 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 25, 25, 25, 25, 25, 37, 37, 91, 127, 201, 201, 201, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 25, 25, 25, 25, 25, 25, 25, 91, 91, 201, 25, 25, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 5, 34, 35, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 554 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451010 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451010 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451010/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451010 Building REAL300024451011 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451011' /scratch/stefan/7786230/working/building/REAL300024451011 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451011 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451011/0 /scratch/stefan/7786230/working/building/REAL300024451011 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/923 `/scratch/stefan/7786230/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=CC=[N+]2[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451011/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451011 none CC1C(NC(=O)C2=CC=CC=[N+]2[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 45, 73, 123, 123, 123, 123, 123, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 45, 45, 123] 123 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 309 number of broken/clashed sets: 22 ./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: REAL300024451011 none CC1C(NC(=O)C2=CC=CC=[N+]2[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 122, 122, 122, 123, 123, 123, 123, 123, 123, 99, 99, 99, 88, 41, 88, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 122, 123, 123, 123, 123, 99, 99, 99, 99, 99, 99, 41, 41, 1] 123 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 388 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451011 none CC1C(NC(=O)C2=CC=CC=[N+]2[O-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 16, 34, 99, 99, 99, 99, 99, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 16, 16, 99] 123 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451011 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451011 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451011/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451011 Building REAL300024451012 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451012' /scratch/stefan/7786230/working/building/REAL300024451012 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451012 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451012/0 /scratch/stefan/7786230/working/building/REAL300024451012 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/924 `/scratch/stefan/7786230/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451012/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451012 none CC1C(NC(=O)C2=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 56, 113, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 56, 56, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 435 number of broken/clashed sets: 25 ./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: REAL300024451012 none CC1C(NC(=O)C2=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 156, 156, 156, 201, 201, 201, 201, 201, 201, 156, 156, 156, 152, 68, 152, 13, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 68, 68, 1] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 639 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451012 none CC1C(NC(=O)C2=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 16, 50, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 16, 16, 156] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 269 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451012 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451012 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451012/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451012 Building REAL300024451013 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451013' /scratch/stefan/7786230/working/building/REAL300024451013 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451013 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451013/0 /scratch/stefan/7786230/working/building/REAL300024451013 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/925 `/scratch/stefan/7786230/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC=C(F)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451013/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451013 none CC1C(NC(=O)C2=CC=C(F)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 15, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 50, 115, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 1, 1, 10, 10, 10, 10, 10, 10, 50, 50, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 423 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: REAL300024451013 none CC1C(NC(=O)C2=CC=C(F)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 15, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 181, 181, 185, 185, 185, 201, 201, 201, 201, 201, 181, 181, 181, 177, 66, 177, 13, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 185, 201, 201, 181, 181, 181, 181, 181, 181, 66, 66, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 577 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451013 none CC1C(NC(=O)C2=CC=C(F)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 15, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 4, 4, 15, 53, 181, 181, 181, 181, 181, 2, 2, 2, 1, 1, 4, 10, 10, 1, 1, 1, 1, 1, 1, 15, 15, 181] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 291 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451013 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451013 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451013/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451013 Building REAL300024451014 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451014' /scratch/stefan/7786230/working/building/REAL300024451014 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451014 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451014/0 /scratch/stefan/7786230/working/building/REAL300024451014 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/926 `/scratch/stefan/7786230/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451014/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451014 none CON=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 183, 183, 183, 136, 136, 136, 136, 136, 121, 31, 121, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 201, 201, 183, 136, 136, 136, 136, 136, 136, 136, 31, 31, 1, 136, 136, 136, 136] 201 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] 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, 39, 40, 41, 42]) total number of confs: 613 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451014 none CON=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 33, 136, 136, 136, 136, 136, 1, 1, 34, 34, 34, 19, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 136, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 285 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451014 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451014 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451014/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451014 Building REAL300024451015 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451015' /scratch/stefan/7786230/working/building/REAL300024451015 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451015 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451015/0 /scratch/stefan/7786230/working/building/REAL300024451015 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/927 `/scratch/stefan/7786230/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451015/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451015 none C#CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 133, 65, 133, 133, 65, 65, 57, 57, 57, 57, 57, 55, 23, 55, 12, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 133, 133, 133, 133, 133, 133, 65, 57, 57, 57, 57, 57, 57, 57, 23, 23, 1, 57, 57, 57, 57] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 879 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451015 none C#CCC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 57, 57, 57, 57, 57, 1, 1, 26, 26, 26, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 57, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451015 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451015 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451015/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451015 Building REAL300024451016 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451016' /scratch/stefan/7786230/working/building/REAL300024451016 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451016 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451016/0 /scratch/stefan/7786230/working/building/REAL300024451016 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/928 `/scratch/stefan/7786230/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CN(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451016/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451016 none CC1C(NC(=O)CN(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 8, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 76, 76, 76, 158, 201, 201, 201, 201, 58, 58, 58, 57, 24, 57, 12, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 76, 158, 158, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 24, 24, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 774 number of broken/clashed sets: 95 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451016 none CC1C(NC(=O)CN(C)C(N)=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 8, 5, 1, 8, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 24, 24, 31, 31, 1, 1, 1, 1, 1, 3, 3, 10, 17, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 16, 16, 24, 24, 24, 31, 31, 1, 1, 1, 1, 1, 1, 10, 10, 58] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451016 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451016 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451016/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451016 Building REAL300024451017 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451017' /scratch/stefan/7786230/working/building/REAL300024451017 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451017 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451017/0 /scratch/stefan/7786230/working/building/REAL300024451017 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/929 `/scratch/stefan/7786230/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451017/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451017 none CC1C(NC(=O)C2=NC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 34, 34, 70, 119, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 12, 1, 22, 22, 22, 22, 22, 22, 70, 70, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 495 number of broken/clashed sets: 9 ./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: REAL300024451017 none CC1C(NC(=O)C2=NC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [109, 109, 109, 109, 119, 119, 119, 201, 201, 201, 201, 201, 109, 109, 109, 107, 40, 107, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 119, 201, 109, 109, 109, 109, 109, 109, 40, 40, 1] 201 rigid atoms, others: [41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 489 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451017 none CC1C(NC(=O)C2=NC(=O)N[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 11, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 3, 3, 11, 29, 109, 109, 109, 109, 109, 2, 2, 2, 1, 1, 5, 22, 1, 1, 1, 1, 1, 1, 11, 11, 109] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 39, 40, 41]) total number of confs: 205 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451017 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451017 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451017/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451017 Building REAL300024451018 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451018' /scratch/stefan/7786230/working/building/REAL300024451018 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451018 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451018/0 /scratch/stefan/7786230/working/building/REAL300024451018 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/930 `/scratch/stefan/7786230/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451018/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451018 none CC1C(NC(=O)C2(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 17, 17, 17, 17, 17, 28, 28, 69, 122, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 69, 69, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 492 number of broken/clashed sets: 14 ./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: REAL300024451018 none CC1C(NC(=O)C2(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [135, 135, 135, 135, 157, 157, 157, 201, 201, 201, 135, 135, 135, 133, 59, 133, 13, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 157, 201, 201, 201, 201, 135, 135, 135, 135, 135, 135, 59, 59, 1] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 670 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451018 none CC1C(NC(=O)C2(F)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 15, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 11, 31, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 11, 11, 135] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 10, 11, 12, 13, 14, 34, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 240 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451018 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451018 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451018/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451018 Building REAL300024451019 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451019' /scratch/stefan/7786230/working/building/REAL300024451019 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451019 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451019/0 /scratch/stefan/7786230/working/building/REAL300024451019 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/931 `/scratch/stefan/7786230/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)(F)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451019/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451019 none CC1C(NC(=O)C(F)(F)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 9, 4, 9, 1, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [32, 33, 34, 35, 36, 6, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 7, 8, 12, 13, 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, 45]) total number of confs: 31 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: REAL300024451019 none CC1C(NC(=O)C(F)(F)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 6, 6, 6, 8, 8, 8, 10, 10, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 1] 10 rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 31 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451019 none CC1C(NC(=O)C(F)(F)C2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 15, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 10, 10, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4] 10 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451019 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451019 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451019/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451019 Building REAL300024451020 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451020' /scratch/stefan/7786230/working/building/REAL300024451020 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451020 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451020/0 /scratch/stefan/7786230/working/building/REAL300024451020 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/932 `/scratch/stefan/7786230/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451020/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451020 none CC1C(NC(=O)COCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 66, 66, 66, 80, 80, 80, 152, 188, 201, 201, 66, 66, 66, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 80, 152, 152, 201, 201, 201, 201, 603, 66, 66, 66, 66, 66, 66, 29, 29, 1] 603 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 1338 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451020 none CC1C(NC(=O)COCCO)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 10, 21, 32, 37, 1, 1, 1, 1, 1, 3, 3, 10, 17, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 3, 10, 10, 32, 32, 37, 37, 111, 1, 1, 1, 1, 1, 1, 10, 10, 66] 603 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451020 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451020 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451020/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451020 Building REAL300024451021 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451021' /scratch/stefan/7786230/working/building/REAL300024451021 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451021 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451021/0 /scratch/stefan/7786230/working/building/REAL300024451021 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/933 `/scratch/stefan/7786230/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NOC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451021/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451021 none CC1C(NC(=O)C2=NOC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 23, 65, 89, 139, 139, 139, 139, 139, 15, 15, 15, 15, 15, 10, 2, 2, 2, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 65, 65, 139] 139 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 40, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 386 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: REAL300024451021 none CC1C(NC(=O)C2=NOC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 85, 85, 85, 124, 124, 124, 139, 139, 139, 139, 139, 139, 85, 85, 85, 81, 38, 81, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 124, 139, 139, 139, 139, 139, 139, 139, 139, 85, 85, 85, 85, 85, 85, 38, 38, 1] 139 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 438 number of broken/clashed sets: 26 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451021 none CC1C(NC(=O)C2=NOC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 16, 32, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 16, 16, 85] 139 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451021 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451021 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451021/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451021 Building REAL300024451022 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451022' /scratch/stefan/7786230/working/building/REAL300024451022 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451022 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451022/0 /scratch/stefan/7786230/working/building/REAL300024451022 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/934 `/scratch/stefan/7786230/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451022/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451022 none CC1C(NC(=O)C2=NC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 28, 41, 74, 74, 74, 74, 74, 9, 9, 9, 9, 9, 4, 1, 1, 9, 9, 9, 9, 9, 9, 28, 28, 74] 74 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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: 178 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: REAL300024451022 none CC1C(NC(=O)C2=NC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 165, 70, 165, 13, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 201, 201, 201, 168, 168, 168, 168, 168, 168, 70, 70, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 631 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451022 none CC1C(NC(=O)C2=NC=C(F)C=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 10, 10, 6, 6, 10, 10, 1, 1, 1, 1, 1, 3, 3, 13, 45, 168, 168, 168, 168, 168, 2, 2, 2, 1, 1, 6, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 168] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 35, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 41, 42, 43]) total number of confs: 284 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451022 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451022 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451022/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451022 Building REAL300024451023 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451023' /scratch/stefan/7786230/working/building/REAL300024451023 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451023 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451023/0 /scratch/stefan/7786230/working/building/REAL300024451023 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/935 `/scratch/stefan/7786230/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(C)(C)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451023/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451023 none CC1C(NC(=O)C(C)(C)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 64, 64, 112, 112, 112, 201, 201, 201, 201, 64, 64, 64, 63, 45, 63, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 112, 201, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 64, 64, 64, 45, 45, 1] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46]) total number of confs: 799 number of broken/clashed sets: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451023 none CC1C(NC(=O)C(C)(C)CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 19, 19, 31, 1, 1, 1, 1, 1, 3, 3, 11, 21, 64, 64, 64, 64, 64, 2, 2, 2, 1, 1, 6, 19, 19, 19, 19, 19, 19, 31, 31, 1, 1, 1, 1, 1, 1, 11, 11, 64] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 11, 12, 13, 14, 44, 43, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451023 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451023 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451023/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451023 Building REAL300024451024 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451024' /scratch/stefan/7786230/working/building/REAL300024451024 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451024 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451024/0 /scratch/stefan/7786230/working/building/REAL300024451024 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/936 `/scratch/stefan/7786230/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451024/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451024 none CC(C)[C@@H](O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 157, 201, 157, 157, 157, 80, 80, 80, 67, 67, 67, 67, 67, 64, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 471, 157, 157, 80, 67, 67, 67, 67, 67, 67, 67, 27, 27, 1, 67, 67, 67, 67] 603 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 1325 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451024 none CC(C)[C@@H](O)CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 20, 32, 14, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 67, 67, 67, 67, 67, 1, 1, 32, 32, 32, 32, 32, 32, 32, 60, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 67, 1, 2, 2, 2] 603 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 324 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451024 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451024 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451024/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451024 Building REAL300024451025 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451025' /scratch/stefan/7786230/working/building/REAL300024451025 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451025 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451025/0 /scratch/stefan/7786230/working/building/REAL300024451025 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/937 `/scratch/stefan/7786230/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024451025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451025/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451025 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 53, 53, 53, 53, 53, 1, 1, 33, 33, 49, 49, 49, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 53, 1, 2, 2, 2, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 200 number of broken/clashed sets: 88 ./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: REAL300024451025 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 192, 105, 105, 105, 53, 53, 53, 53, 53, 51, 39, 51, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 192, 192, 201, 201, 201, 105, 53, 53, 53, 53, 53, 53, 53, 39, 39, 1, 53, 53, 53, 53, 192, 192, 192, 192] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 645 number of broken/clashed sets: 88 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451025 none CSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 1, 1, 10, 10, 10, 33, 33, 33, 33, 33, 49, 49, 99, 145, 192, 192, 192, 192, 192, 33, 33, 1, 1, 7, 7, 7, 10, 33, 33, 33, 33, 33, 33, 33, 99, 99, 192, 33, 33, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 43, 44, 45, 46, 23, 24] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 569 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451025 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451025 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451025/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451025 Building REAL300024451026 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451026' /scratch/stefan/7786230/working/building/REAL300024451026 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451026 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451026/0 /scratch/stefan/7786230/working/building/REAL300024451026 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/938 `/scratch/stefan/7786230/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451026/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451026 none CC1C(NC(=O)C2=NOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 10, 10, 1, 10, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 24, 24, 73, 138, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 10, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 73, 73, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 485 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: REAL300024451026 none CC1C(NC(=O)C2=NOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 163, 163, 163, 173, 173, 173, 201, 201, 201, 201, 163, 163, 163, 159, 61, 159, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 173, 201, 201, 201, 201, 163, 163, 163, 163, 163, 163, 61, 61, 1] 201 rigid atoms, others: [43, 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: 561 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451026 none CC1C(NC(=O)C2=NOCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 14, 47, 163, 163, 163, 163, 163, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 14, 14, 163] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 273 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451026 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451026 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451026/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451026 Building REAL300024451027 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451027' /scratch/stefan/7786230/working/building/REAL300024451027 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451027 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451027/0 /scratch/stefan/7786230/working/building/REAL300024451027 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/939 `/scratch/stefan/7786230/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(CCO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451027/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451027 none CC1C(NC(=O)C2(CCO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 7, 7, 1, 7, 1, 1, 7, 12, 1, 1, 14, 14, 14, 14, 14, 18, 18, 39, 68, 142, 142, 142, 142, 142, 14, 14, 14, 14, 14, 7, 7, 7, 12, 12, 36, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 39, 39, 142] 603 rigid atoms, others: [4, 37, 6, 7, 40, 10, 11, 39, 38] set([0, 1, 2, 3, 5, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 392 number of broken/clashed sets: 40 ./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: REAL300024451027 none CC1C(NC(=O)C2(CCO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 70, 70, 70, 87, 87, 87, 142, 201, 201, 142, 142, 70, 70, 70, 68, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 87, 201, 201, 201, 201, 603, 142, 142, 142, 142, 70, 70, 70, 70, 70, 70, 28, 28, 1] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1428 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451027 none CC1C(NC(=O)C2(CCO)CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 6, 6, 6, 14, 30, 37, 14, 14, 1, 1, 1, 1, 1, 3, 3, 10, 20, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 6, 30, 30, 37, 37, 111, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 10, 10, 70] 603 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 374 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451027 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451027 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451027/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451027 Building REAL300024451028 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451028' /scratch/stefan/7786230/working/building/REAL300024451028 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451028 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451028/0 /scratch/stefan/7786230/working/building/REAL300024451028 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/940 `/scratch/stefan/7786230/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451028/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451028 none CC(C)C(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3] 9 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 13 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451028 none CC(C)C(C)(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2] 9 rigid atoms, others: [43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451028 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451028 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451028/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451028 Building REAL300024451029 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451029' /scratch/stefan/7786230/working/building/REAL300024451029 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451029 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451029/0 /scratch/stefan/7786230/working/building/REAL300024451029 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/941 `/scratch/stefan/7786230/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451029/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451029 none CC1C(NC(=O)C2(C)CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 51, 98, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 6, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 51, 51, 201] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 443 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: REAL300024451029 none CC1C(NC(=O)C2(C)CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 80, 80, 80, 201, 201, 201, 201, 201, 201, 78, 78, 78, 76, 41, 76, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 78, 41, 41, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 593 number of broken/clashed sets: 201 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451029 none CC1C(NC(=O)C2(C)CC(C)(C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 12, 28, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 78] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 13, 14, 47, 16, 49, 50, 51, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451029 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451029 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451029/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451029 Building REAL300024451030 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451030' /scratch/stefan/7786230/working/building/REAL300024451030 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451030 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451030/0 /scratch/stefan/7786230/working/building/REAL300024451030 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/942 `/scratch/stefan/7786230/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCSC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451030/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451030 none CC1CCSC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 31, 103, 103, 103, 103, 103, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 103, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 201 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: REAL300024451030 none CC1CCSC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 131, 131, 131, 103, 103, 103, 103, 103, 101, 48, 101, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 103, 103, 103, 103, 103, 103, 103, 48, 48, 1, 103, 103, 103, 103] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 659 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451030 none CC1CCSC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 13, 13, 13, 13, 13, 21, 21, 61, 116, 201, 201, 201, 201, 201, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 61, 61, 201, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 475 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451030 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451030 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451030/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451030 Building REAL300024451031 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451031' /scratch/stefan/7786230/working/building/REAL300024451031 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451031 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451031/0 /scratch/stefan/7786230/working/building/REAL300024451031 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/943 `/scratch/stefan/7786230/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451031/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451031 none CC(C[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [199, 187, 199, 201, 201, 201, 201, 187, 187, 116, 116, 116, 116, 116, 101, 30, 101, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 187, 116, 116, 116, 116, 116, 116, 116, 30, 30, 1, 116, 116, 116, 116] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53]) total number of confs: 645 number of broken/clashed sets: 191 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451031 none CC(C[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 17, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 27, 116, 116, 116, 116, 116, 1, 1, 17, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 116, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 40, 9, 10, 11, 12, 13, 14, 44, 50, 46, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 51, 52, 53]) total number of confs: 260 number of broken/clashed sets: 191 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451031 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451031 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451031/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451031 Building REAL300024451032 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451032' /scratch/stefan/7786230/working/building/REAL300024451032 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451032 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451032/0 /scratch/stefan/7786230/working/building/REAL300024451032 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/944 `/scratch/stefan/7786230/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451032/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451032 none CC1C(NC(=O)CC2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 22, 22, 8, 22, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 43, 43, 83, 121, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 22, 8, 8, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31, 83, 83, 201] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 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, 44, 45, 46, 47]) total number of confs: 547 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: REAL300024451032 none CC1C(NC(=O)CC2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 81, 81, 107, 107, 107, 193, 201, 201, 201, 201, 201, 81, 81, 81, 81, 30, 81, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 107, 193, 193, 201, 201, 201, 201, 81, 81, 81, 81, 81, 81, 30, 30, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 792 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451032 none CC1C(NC(=O)CC2=CN(C)N=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 8, 5, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 19, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 9, 16, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 4, 19, 19, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 9, 9, 81] 201 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451032 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451032 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451032/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451032 Building REAL300024451033 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451033' /scratch/stefan/7786230/working/building/REAL300024451033 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451033 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451033/0 /scratch/stefan/7786230/working/building/REAL300024451033 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/945 `/scratch/stefan/7786230/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451033/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451033 none CC1C(NC(=O)C2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 58, 116, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 4, 1, 11, 11, 11, 11, 11, 11, 58, 58, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 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]) total number of confs: 443 number of broken/clashed sets: 22 ./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: REAL300024451033 none CC1C(NC(=O)C2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 165, 165, 165, 195, 195, 195, 201, 201, 201, 201, 165, 165, 165, 159, 64, 159, 13, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 195, 201, 165, 165, 165, 165, 165, 165, 64, 64, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 609 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451033 none CC1C(NC(=O)C2=NN=CS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 8, 1, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 16, 50, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 6, 11, 1, 1, 1, 1, 1, 1, 16, 16, 165] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 32, 11, 12, 13, 14, 15, 34, 35, 28, 29, 37] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 38, 39, 40]) total number of confs: 277 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451033 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451033 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451033/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451033 Building REAL300024451034 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451034' /scratch/stefan/7786230/working/building/REAL300024451034 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451034 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451034/0 /scratch/stefan/7786230/working/building/REAL300024451034 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/946 `/scratch/stefan/7786230/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2[C@H]3CCCO[C@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451034/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451034 none CC1C(NC(=O)[C@@H]2[C@H]3CCCO[C@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 25, 25, 80, 124, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 12, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 80, 80, 201] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 506 number of broken/clashed sets: 34 ./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: REAL300024451034 none CC1C(NC(=O)[C@@H]2[C@H]3CCCO[C@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 73, 74, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 69, 40, 69, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 74, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 73, 40, 40, 1] 201 rigid atoms, others: [50, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 599 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451034 none CC1C(NC(=O)[C@@H]2[C@H]3CCCO[C@H]32)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 14, 25, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 14, 14, 73] 201 rigid atoms, others: [0, 1, 2, 3, 33, 42, 43, 44, 34, 46, 45, 16, 17, 18, 19, 20, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451034 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451034 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451034/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451034 Building REAL300024451035 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451035' /scratch/stefan/7786230/working/building/REAL300024451035 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451035 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451035/0 /scratch/stefan/7786230/working/building/REAL300024451035 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/947 `/scratch/stefan/7786230/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)SN=C1) `REAL300024451035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451035/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451035 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)SN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 32, 96, 96, 96, 96, 96, 1, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 96, 1, 2, 2, 2, 14] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 18 ./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: REAL300024451035 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)SN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 121, 121, 121, 96, 96, 96, 96, 96, 91, 45, 91, 13, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 201, 201, 201, 201, 121, 96, 96, 96, 96, 96, 96, 96, 45, 45, 1, 96, 96, 96, 96, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44]) total number of confs: 532 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451035 none CC1=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)SN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 14, 14, 14, 14, 14, 22, 22, 59, 110, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 14, 14, 14, 59, 59, 201, 14, 14, 14, 14, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 464 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451035 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451035 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451035/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451035 Building REAL300024451036 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451036' /scratch/stefan/7786230/working/building/REAL300024451036 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451036 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451036/0 /scratch/stefan/7786230/working/building/REAL300024451036 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/948 `/scratch/stefan/7786230/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451036/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451036 none CC1C(NC(=O)C(F)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 21, 21, 6, 21, 1, 6, 1, 1, 1, 1, 32, 32, 32, 32, 32, 44, 44, 88, 132, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 21, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 88, 88, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 520 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: REAL300024451036 none CC1C(NC(=O)C(F)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 93, 93, 93, 132, 132, 132, 147, 147, 201, 201, 201, 93, 93, 93, 87, 30, 87, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 132, 147, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 93, 30, 30, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 702 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451036 none CC1C(NC(=O)C(F)C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 15, 15, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 11, 25, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 6, 15, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 11, 11, 93] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451036 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451036 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451036/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451036 Building REAL300024451037 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451037' /scratch/stefan/7786230/working/building/REAL300024451037 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451037 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451037/0 /scratch/stefan/7786230/working/building/REAL300024451037 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/949 `/scratch/stefan/7786230/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451037/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451037 none CC(OC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 7, 7, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5] 7 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 16 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451037 none CC(OC(F)F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 6, 7, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451037 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451037 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451037/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451037 Building REAL300024451038 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451038' /scratch/stefan/7786230/working/building/REAL300024451038 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451038 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451038/0 /scratch/stefan/7786230/working/building/REAL300024451038 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/950 `/scratch/stefan/7786230/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451038/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451038 none CC1C(NC(=O)C2CC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 18, 18, 54, 76, 119, 119, 119, 119, 119, 13, 13, 13, 13, 13, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 54, 54, 119] 119 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 329 number of broken/clashed sets: 22 ./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: REAL300024451038 none CC1C(NC(=O)C2CC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 91, 91, 91, 119, 119, 119, 119, 119, 79, 79, 79, 76, 37, 76, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 91, 119, 119, 119, 119, 119, 119, 119, 119, 119, 79, 79, 79, 79, 79, 79, 37, 37, 1] 119 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 395 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451038 none CC1C(NC(=O)C2CC(C)(C)O2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 15, 30, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 15, 15, 79] 119 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451038 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451038 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451038/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451038 Building REAL300024451039 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451039' /scratch/stefan/7786230/working/building/REAL300024451039 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451039 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451039/0 /scratch/stefan/7786230/working/building/REAL300024451039 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/951 `/scratch/stefan/7786230/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024451039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451039/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451039 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 30, 73, 73, 73, 73, 73, 1, 1, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 73, 1, 2, 2, 2] 109 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44]) total number of confs: 163 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: REAL300024451039 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 89, 89, 89, 73, 73, 73, 73, 73, 70, 38, 70, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 109, 109, 109, 109, 89, 73, 73, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 73, 73] 109 rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451039 none C#CC1=CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 12, 12, 12, 12, 12, 17, 17, 47, 71, 109, 109, 109, 109, 109, 12, 12, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 47, 47, 109, 12, 12, 12, 12] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451039 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451039 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451039/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451039 Building REAL300024451040 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451040' /scratch/stefan/7786230/working/building/REAL300024451040 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451040 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451040/0 /scratch/stefan/7786230/working/building/REAL300024451040 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/952 `/scratch/stefan/7786230/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1) `REAL300024451040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451040/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451040 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 19, 53, 53, 53, 53, 53, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 53, 1, 2, 2, 2] 83 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 128 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: REAL300024451040 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 58, 58, 58, 53, 53, 53, 53, 53, 50, 32, 50, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 83, 83, 83, 83, 83, 83, 83, 83, 58, 53, 53, 53, 53, 53, 53, 53, 32, 32, 1, 53, 53, 53, 53] 83 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] 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, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 15 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451040 none CC1CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 16, 16, 16, 16, 16, 24, 24, 47, 59, 83, 83, 83, 83, 83, 16, 16, 1, 1, 2, 2, 2, 1, 1, 1, 11, 16, 16, 16, 16, 16, 16, 16, 47, 47, 83, 16, 16, 16, 16] 83 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451040 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451040 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451040/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451040 Building REAL300024451041 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451041' /scratch/stefan/7786230/working/building/REAL300024451041 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451041 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451041/0 /scratch/stefan/7786230/working/building/REAL300024451041 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/953 `/scratch/stefan/7786230/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(C)(C)N=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451041/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451041 none CC1C(NC(=O)CC(C)(C)N=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 93, 93, 93, 159, 168, 168, 168, 201, 201, 75, 75, 75, 72, 27, 72, 11, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 93, 159, 159, 168, 168, 168, 168, 168, 168, 75, 75, 75, 75, 75, 75, 27, 27, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 717 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451041 none CC1C(NC(=O)CC(C)(C)N=[N+]=[N-])CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 11, 18, 18, 18, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 4, 11, 11, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 10, 10, 75] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451041 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451041 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451041/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451041 Building REAL300024451042 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451042' /scratch/stefan/7786230/working/building/REAL300024451042 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451042 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451042/0 /scratch/stefan/7786230/working/building/REAL300024451042 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/954 `/scratch/stefan/7786230/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(C)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451042/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451042 none CC1C(NC(=O)C2CC(C)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 22, 22, 77, 118, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 11, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16, 77, 77, 201] 201 rigid atoms, others: [32, 33, 34, 4, 38, 6, 7, 8, 9, 10, 11, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 504 number of broken/clashed sets: 44 ./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: REAL300024451042 none CC1C(NC(=O)C2CC(C)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [83, 83, 83, 83, 84, 84, 84, 201, 201, 201, 201, 201, 83, 83, 83, 77, 44, 77, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 84, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 83, 83, 83, 44, 44, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 619 number of broken/clashed sets: 44 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451042 none CC1C(NC(=O)C2CC(C)(F)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 14, 26, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 14, 14, 83] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451042 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451042 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451042/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451042 Building REAL300024451043 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451043' /scratch/stefan/7786230/working/building/REAL300024451043 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451043 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451043/0 /scratch/stefan/7786230/working/building/REAL300024451043 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/955 `/scratch/stefan/7786230/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451043/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451043 none CC1C(NC(=O)CC(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 40, 40, 26, 40, 6, 6, 6, 1, 1, 1, 1, 48, 48, 48, 48, 48, 68, 68, 97, 137, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 40, 26, 26, 6, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 97, 97, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 604 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: REAL300024451043 none CC1C(NC(=O)CC(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 52, 52, 52, 69, 69, 69, 152, 165, 165, 165, 201, 201, 52, 52, 52, 52, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 69, 152, 152, 165, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 52, 26, 26, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 797 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451043 none CC1C(NC(=O)CC(=O)NC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 21, 21, 21, 48, 48, 1, 1, 1, 1, 1, 3, 3, 8, 15, 52, 52, 52, 52, 52, 2, 2, 2, 1, 1, 3, 14, 14, 21, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 8, 8, 52] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451043 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451043 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451043/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451043 Building REAL300024451044 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451044' /scratch/stefan/7786230/working/building/REAL300024451044 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451044 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451044/0 /scratch/stefan/7786230/working/building/REAL300024451044 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/956 `/scratch/stefan/7786230/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451044/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451044 none COCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 190, 116, 190, 116, 116, 104, 104, 104, 104, 104, 99, 31, 99, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 201, 201, 190, 570, 116, 104, 104, 104, 104, 104, 104, 104, 31, 31, 1, 104, 104, 104, 104] 603 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 1303 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451044 none COCC(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 25, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 27, 104, 104, 104, 104, 104, 1, 1, 34, 34, 34, 25, 25, 13, 39, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 104, 1, 2, 2, 2] 603 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 323 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451044 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451044 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451044/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451044 Building REAL300024451045 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451045' /scratch/stefan/7786230/working/building/REAL300024451045 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451045 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451045/0 /scratch/stefan/7786230/working/building/REAL300024451045 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/957 `/scratch/stefan/7786230/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1) `REAL300024451045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451045/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451045 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 87, 87, 87, 87, 87, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 87, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 40, 41, 23, 24, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 40 ./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: REAL300024451045 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 115, 115, 115, 87, 87, 87, 87, 87, 80, 38, 80, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 87, 87, 87, 87, 87, 87, 87, 38, 38, 1, 87, 87, 87, 87] 201 rigid atoms, others: [45, 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, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 657 number of broken/clashed sets: 40 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451045 none CC1CCC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)S1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 20, 20, 20, 20, 20, 33, 33, 94, 131, 201, 201, 201, 201, 201, 20, 20, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 20, 20, 20, 94, 94, 201, 20, 20, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 565 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451045 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451045 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451045/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451045 Building REAL300024451046 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451046' /scratch/stefan/7786230/working/building/REAL300024451046 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451046 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451046/0 /scratch/stefan/7786230/working/building/REAL300024451046 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/958 `/scratch/stefan/7786230/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451046/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451046 none C#CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 90, 201, 201, 90, 90, 84, 84, 84, 84, 84, 82, 40, 82, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 90, 84, 84, 84, 84, 84, 84, 84, 40, 40, 1, 84, 84, 84, 84] 201 rigid atoms, others: [42, 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, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 824 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451046 none C#CC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 28, 84, 84, 84, 84, 84, 1, 1, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 84, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451046 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451046 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451046/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451046 Building REAL300024451047 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451047' /scratch/stefan/7786230/working/building/REAL300024451047 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451047 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451047/0 /scratch/stefan/7786230/working/building/REAL300024451047 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/959 `/scratch/stefan/7786230/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451047/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451047 none CC1C(NC(=O)C=CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 25, 25, 8, 25, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 39, 39, 87, 122, 201, 201, 201, 201, 201, 28, 28, 28, 28, 28, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 87, 87, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 527 number of broken/clashed sets: 35 ./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: REAL300024451047 none CC1C(NC(=O)C=CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 70, 70, 72, 72, 72, 194, 194, 201, 201, 201, 201, 70, 70, 70, 68, 39, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 72, 194, 194, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 70, 39, 39, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 592 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451047 none CC1C(NC(=O)C=CC2CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 13, 23, 70, 70, 70, 70, 70, 2, 2, 2, 1, 1, 3, 14, 14, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 13, 13, 70] 201 rigid atoms, others: [0, 1, 2, 3, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 47, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451047 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451047 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451047/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451047 Building REAL300024451048 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451048' /scratch/stefan/7786230/working/building/REAL300024451048 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451048 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451048/0 /scratch/stefan/7786230/working/building/REAL300024451048 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/960 `/scratch/stefan/7786230/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451048/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451048 none COC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 177, 199, 121, 177, 121, 121, 100, 100, 100, 100, 100, 96, 30, 96, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 201, 201, 201, 201, 201, 177, 531, 121, 100, 100, 100, 100, 100, 100, 100, 30, 30, 1, 100, 100, 100, 100] 603 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 1337 number of broken/clashed sets: 28 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451048 none COC(C)C(O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 21, 14, 19, 3, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 100, 100, 100, 100, 100, 1, 1, 27, 27, 27, 21, 21, 21, 21, 14, 42, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 100, 1, 2, 2, 2] 603 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 46, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 47, 48, 49]) total number of confs: 308 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451048 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451048 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451048/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451048 Building REAL300024451049 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451049' /scratch/stefan/7786230/working/building/REAL300024451049 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451049 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451049/0 /scratch/stefan/7786230/working/building/REAL300024451049 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/961 `/scratch/stefan/7786230/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451049/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451049 none CC1C(NC(=O)[C@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 19, 19, 59, 111, 201, 201, 201, 201, 201, 13, 13, 13, 13, 13, 10, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 59, 59, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 453 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: REAL300024451049 none CC1C(NC(=O)[C@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [150, 150, 150, 150, 167, 167, 167, 201, 201, 201, 201, 201, 201, 150, 150, 150, 146, 63, 146, 12, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 167, 201, 201, 201, 201, 150, 150, 150, 150, 150, 150, 63, 63, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 626 number of broken/clashed sets: 11 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451049 none CC1C(NC(=O)[C@H]2CNC(=O)N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 15, 42, 150, 150, 150, 150, 150, 2, 2, 2, 1, 1, 3, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 15, 15, 150] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451049 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451049 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451049/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451049 Building REAL300024451050 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451050' /scratch/stefan/7786230/working/building/REAL300024451050 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451050 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451050/0 /scratch/stefan/7786230/working/building/REAL300024451050 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/962 `/scratch/stefan/7786230/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451050/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451050 none CCSC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 100, 177, 100, 100, 77, 77, 77, 77, 77, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 177, 177, 177, 177, 100, 77, 77, 77, 77, 77, 77, 77, 30, 30, 1, 77, 77, 77, 77] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 718 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451050 none CCSC(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 26, 11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 20, 77, 77, 77, 77, 77, 1, 1, 31, 31, 31, 31, 31, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 77, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451050 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451050 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451050/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451050 Building REAL300024451051 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451051' /scratch/stefan/7786230/working/building/REAL300024451051 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300024451051 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451051/0 /scratch/stefan/7786230/working/building/REAL300024451051 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/963 `/scratch/stefan/7786230/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CC(C)C1) `REAL300024451051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451051/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 123, 123, 123, 109, 109, 109, 109, 109, 94, 30, 94, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 109, 109, 109, 109, 109, 109, 109, 30, 30, 1, 109, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 729 number of broken/clashed sets: 25 ./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: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 11, 11, 11, 15, 15, 15, 15, 15, 26, 26, 84, 125, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 15, 15, 15, 15, 15, 15, 15, 84, 84, 201, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 52, 53, 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, 49, 50, 51]) total number of confs: 542 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 27, 109, 109, 109, 109, 109, 1, 1, 13, 15, 15, 15, 15, 13, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 109, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451051 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024451051/1 /scratch/stefan/7786230/working/building/REAL300024451051 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/964 `/scratch/stefan/7786230/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CC(C)C1) `REAL300024451051.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024451051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451051/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 18, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 9 ./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: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 12, 14, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 12, 12, 21, 6, 6, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1] 21 rigid atoms, others: [1, 54, 47, 48, 49, 53, 22, 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 9 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451051 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 21, 21, 21, 21, 21, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 21 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 43, 20, 21, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451051 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451051 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451051/0.* 1: /scratch/stefan/7786230/working/building/REAL300024451051/1.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451051 Building REAL300024451052 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451052' /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300024451052 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451052/0 /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/965 `/scratch/stefan/7786230/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451052/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 24, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 24, 97, 97, 97, 97, 97, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 97, 1, 2, 2, 2] 201 rigid atoms, others: [43, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 48, 49, 50]) total number of confs: 226 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: REAL300024451052 none CC1CCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 200, 107, 107, 107, 97, 97, 97, 97, 97, 87, 28, 87, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 107, 97, 97, 97, 97, 97, 97, 97, 28, 28, 1, 97, 97, 97, 97] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 728 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CCN1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 18, 18, 18, 24, 24, 24, 24, 24, 38, 38, 91, 131, 201, 201, 201, 201, 201, 24, 24, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 18, 24, 24, 24, 24, 24, 24, 24, 91, 91, 201, 24, 24, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 565 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `1' /scratch/stefan/7786230/working/building/REAL300024451052/1 /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/966 `/scratch/stefan/7786230/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451052.mol2' -> `1.mol2' `temp.mol2' -> `REAL300024451052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451052/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 30, 30, 20, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 27, 90, 90, 90, 90, 90, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 90, 1, 2, 2, 2] 201 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 24 ./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: REAL300024451052 none CC1CC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 129, 129, 129, 90, 90, 90, 90, 90, 83, 29, 83, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 90, 90, 90, 90, 90, 90, 90, 29, 29, 1, 90, 90, 90, 90] 201 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 763 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CC[N@@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 15, 15, 15, 30, 30, 30, 30, 30, 48, 48, 101, 140, 201, 201, 201, 201, 201, 30, 30, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 15, 30, 30, 30, 30, 30, 30, 30, 101, 101, 201, 30, 30, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 560 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 mkdir: created directory `2' /scratch/stefan/7786230/working/building/REAL300024451052/2 /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 2 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/967 `/scratch/stefan/7786230/working/3D/967' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451052.mol2' -> `2.mol2' `temp.mol2' -> `REAL300024451052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451052/2/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 13, 9, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 23, 23, 23, 23, 23, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 1, 2, 2, 2] 32 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 48, 41, 25, 26, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 92 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: REAL300024451052 none CC1CC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 32, 25, 25, 25, 23, 23, 23, 23, 23, 23, 18, 23, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 30, 30, 25, 23, 23, 23, 23, 23, 23, 23, 18, 18, 1, 23, 23, 23, 23] 32 rigid atoms, others: [47, 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, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 21 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451052 none CC1CC[N@H+]1CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 22, 25, 32, 32, 32, 32, 32, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 11, 13, 13, 13, 13, 13, 13, 13, 22, 22, 32, 13, 13, 13, 13] 32 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451052 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451052 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451052/0.* 1: /scratch/stefan/7786230/working/building/REAL300024451052/1.* 2: /scratch/stefan/7786230/working/building/REAL300024451052/2.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451052 Building REAL300024451053 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451053' /scratch/stefan/7786230/working/building/REAL300024451053 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451053 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451053/0 /scratch/stefan/7786230/working/building/REAL300024451053 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/968 `/scratch/stefan/7786230/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1) `REAL300024451053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451053/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451053 none COC(C)(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 71, 74, 71, 71, 42, 42, 42, 42, 42, 40, 36, 40, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 74, 74, 74, 74, 74, 74, 74, 74, 74, 71, 42, 42, 42, 42, 42, 42, 42, 36, 36, 1, 42, 42, 42, 42, 74, 74, 74, 74, 74] 74 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 254 number of broken/clashed sets: 35 ./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: REAL300024451053 none COC(C)(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 3, 6, 6, 6, 14, 14, 14, 14, 14, 21, 21, 37, 54, 74, 74, 74, 74, 74, 14, 14, 1, 1, 1, 5, 5, 5, 3, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 37, 37, 74, 14, 14, 14, 14, 1, 1, 1, 1, 1] 74 rigid atoms, others: [2, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451053 none COC(C)(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 6, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 42, 42, 42, 42, 42, 1, 1, 14, 14, 14, 15, 15, 15, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 1, 2, 2, 2, 14, 14, 14, 14, 14] 74 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 40, 22, 23, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451053 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451053 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451053/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451053 Building REAL300024451054 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451054' /scratch/stefan/7786230/working/building/REAL300024451054 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451054 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451054/0 /scratch/stefan/7786230/working/building/REAL300024451054 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/969 `/scratch/stefan/7786230/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)COC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451054/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451054 none CC1C(NC(=O)COC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 35, 35, 18, 35, 5, 1, 1, 1, 1, 41, 41, 41, 41, 41, 51, 51, 94, 130, 201, 201, 201, 201, 201, 41, 41, 41, 41, 41, 35, 18, 18, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 94, 94, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 569 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: REAL300024451054 none CC1C(NC(=O)COC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 91, 91, 91, 153, 171, 201, 201, 75, 75, 75, 71, 29, 71, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 91, 153, 153, 201, 201, 201, 201, 201, 75, 75, 75, 75, 75, 75, 29, 29, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 757 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451054 none CC1C(NC(=O)COC2CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 23, 41, 41, 1, 1, 1, 1, 1, 3, 3, 10, 17, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 3, 9, 9, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 10, 10, 75] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 235 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451054 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451054 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451054/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451054 Building REAL300024451055 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451055' /scratch/stefan/7786230/working/building/REAL300024451055 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451055 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451055/0 /scratch/stefan/7786230/working/building/REAL300024451055 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/970 `/scratch/stefan/7786230/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451055/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451055 none CC1C(NC(=O)C2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 41, 87, 155, 155, 155, 155, 155, 6, 6, 6, 6, 6, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 41, 41, 155] 155 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 326 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: REAL300024451055 none CC1C(NC(=O)C2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 50, 13, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 1] 50 rigid atoms, others: [42, 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]) total number of confs: 160 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451055 none CC1C(NC(=O)C2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 12, 25, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 3, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 50] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451055 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451055 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451055/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451055 Building REAL300024451056 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451056' /scratch/stefan/7786230/working/building/REAL300024451056 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451056 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451056/0 /scratch/stefan/7786230/working/building/REAL300024451056 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/971 `/scratch/stefan/7786230/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451056/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451056 none CC1C(NC(=O)C=CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 28, 28, 8, 28, 8, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 41, 41, 85, 116, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 85, 85, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 500 number of broken/clashed sets: 24 ./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: REAL300024451056 none CC1C(NC(=O)C=CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 65, 65, 65, 66, 66, 66, 144, 144, 201, 201, 201, 65, 65, 65, 65, 33, 65, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 66, 144, 144, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 65, 65, 65, 33, 33, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 695 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451056 none CC1C(NC(=O)C=CC2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 30, 30, 30, 1, 1, 1, 1, 1, 3, 3, 9, 16, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 3, 11, 11, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 9, 9, 65] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451056 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451056 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451056/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451056 Building REAL300024451057 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451057' /scratch/stefan/7786230/working/building/REAL300024451057 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451057 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451057/0 /scratch/stefan/7786230/working/building/REAL300024451057 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/972 `/scratch/stefan/7786230/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1) `REAL300024451057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451057/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451057 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 41, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 17 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: REAL300024451057 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [40, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 7 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451057 none COC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451057 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451057 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451057/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451057 Building REAL300024451058 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451058' /scratch/stefan/7786230/working/building/REAL300024451058 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451058 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451058/0 /scratch/stefan/7786230/working/building/REAL300024451058 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/973 `/scratch/stefan/7786230/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451058/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451058 none CC1C(NC(=O)C2=CC(=O)NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 26, 26, 60, 108, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 9, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 16, 60, 60, 201] 201 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 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, 44, 45, 46]) total number of confs: 471 number of broken/clashed sets: 14 ./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: REAL300024451058 none CC1C(NC(=O)C2=CC(=O)NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 148, 148, 148, 201, 201, 201, 201, 201, 201, 98, 98, 98, 96, 47, 96, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 148, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 47, 47, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451058 none CC1C(NC(=O)C2=CC(=O)NN2C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 15, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 11, 29, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 11, 11, 98] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 190 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451058 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451058 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451058/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451058 Building REAL300024451059 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451059' /scratch/stefan/7786230/working/building/REAL300024451059 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451059 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451059/0 /scratch/stefan/7786230/working/building/REAL300024451059 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/974 `/scratch/stefan/7786230/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024451059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451059/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451059 none CCC1=CNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 100, 100, 100, 100, 100, 1, 1, 13, 27, 27, 27, 27, 27, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 100, 1, 2, 2, 2, 13] 198 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 268 number of broken/clashed sets: 34 ./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: REAL300024451059 none CCC1=CNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 151, 151, 151, 151, 139, 139, 139, 100, 100, 100, 100, 100, 90, 41, 90, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 151, 198, 198, 198, 198, 198, 151, 151, 139, 100, 100, 100, 100, 100, 100, 100, 41, 41, 1, 100, 100, 100, 100, 151] 198 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 762 number of broken/clashed sets: 34 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451059 none CCC1=CNC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 20, 20, 44, 64, 151, 151, 151, 151, 151, 13, 13, 1, 5, 5, 5, 4, 4, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 44, 44, 151, 13, 13, 13, 13, 1] 198 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 347 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451059 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451059 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451059/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451059 Building REAL300024451060 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451060' /scratch/stefan/7786230/working/building/REAL300024451060 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451060 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451060/0 /scratch/stefan/7786230/working/building/REAL300024451060 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/975 `/scratch/stefan/7786230/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451060/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451060 none CCCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 154, 154, 81, 81, 81, 76, 76, 76, 76, 76, 66, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 154, 154, 81, 76, 76, 76, 76, 76, 76, 76, 27, 27, 1, 76, 76, 76, 76] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 769 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451060 none CCCC=CC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 23, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 76, 76, 76, 76, 76, 1, 1, 29, 29, 29, 29, 29, 23, 23, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 76, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451060 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451060 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451060/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451060 Building REAL300024451061 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451061' /scratch/stefan/7786230/working/building/REAL300024451061 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451061 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451061/0 /scratch/stefan/7786230/working/building/REAL300024451061 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/976 `/scratch/stefan/7786230/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451061/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451061 none CC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 193, 201, 193, 193, 158, 158, 158, 158, 158, 153, 65, 153, 13, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 193, 158, 158, 158, 158, 158, 158, 158, 65, 65, 1, 158, 158, 158, 158] 201 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] 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, 39, 40, 41, 42]) total number of confs: 626 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451061 none CC=C(F)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 6, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 44, 158, 158, 158, 158, 158, 1, 1, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 158, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 272 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451061 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451061 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451061/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451061 Building REAL300024451062 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451062' /scratch/stefan/7786230/working/building/REAL300024451062 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451062 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451062/0 /scratch/stefan/7786230/working/building/REAL300024451062 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/977 `/scratch/stefan/7786230/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=NSNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451062/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451062 none CC1C(NC(=O)C2=NSNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 28, 28, 59, 102, 201, 201, 201, 201, 201, 18, 18, 18, 18, 18, 12, 1, 18, 18, 18, 18, 18, 18, 59, 59, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 463 number of broken/clashed sets: 25 ./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: REAL300024451062 none CC1C(NC(=O)C2=NSNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 65, 65, 65, 201, 201, 201, 201, 201, 58, 58, 58, 58, 36, 58, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 65, 201, 58, 58, 58, 58, 58, 58, 36, 36, 1] 201 rigid atoms, others: [41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 388 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451062 none CC1C(NC(=O)C2=NSNC2=O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 8, 14, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 10, 21, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 18, 1, 1, 1, 1, 1, 1, 10, 10, 58] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451062 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451062 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451062/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451062 Building REAL300024451063 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451063' /scratch/stefan/7786230/working/building/REAL300024451063 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451063 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451063/0 /scratch/stefan/7786230/working/building/REAL300024451063 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/978 `/scratch/stefan/7786230/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C) `REAL300024451063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451063/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451063 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [42, 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, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 5 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451063 none CCC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 11, 43, 21, 22, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451063 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451063 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451063/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451063 Building REAL300024451064 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451064' /scratch/stefan/7786230/working/building/REAL300024451064 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451064 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451064/0 /scratch/stefan/7786230/working/building/REAL300024451064 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/979 `/scratch/stefan/7786230/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451064/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451064 none CSC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 186, 112, 186, 186, 112, 112, 70, 70, 70, 70, 70, 68, 49, 68, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 201, 201, 201, 186, 186, 186, 186, 186, 186, 112, 70, 70, 70, 70, 70, 70, 70, 49, 49, 1, 70, 70, 70, 70] 201 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 817 number of broken/clashed sets: 54 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451064 none CSC(C)(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 70, 70, 70, 70, 70, 1, 1, 27, 27, 27, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 70, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451064 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451064 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451064/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451064 Building REAL300024451065 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451065' /scratch/stefan/7786230/working/building/REAL300024451065 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451065 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451065/0 /scratch/stefan/7786230/working/building/REAL300024451065 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/980 `/scratch/stefan/7786230/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2=CN=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451065/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451065 none CC1C(NC(=O)CC2=CN=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 8, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 30, 30, 34, 35, 42, 42, 42, 42, 42, 28, 28, 28, 28, 28, 23, 5, 5, 1, 28, 28, 28, 28, 28, 28, 34, 34, 42] 42 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 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: REAL300024451065 none CC1C(NC(=O)CC2=CN=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 8, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 10, 10, 10, 24, 42, 42, 42, 42, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 24, 24, 42, 8, 8, 8, 8, 8, 8, 8, 8, 1] 42 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 19 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451065 none CC1C(NC(=O)CC2=CN=NS2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 1, 11, 5, 1, 1, 8, 8, 14, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 13, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 3, 13, 13, 28, 1, 1, 1, 1, 1, 1, 5, 5, 8] 42 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451065 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451065 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451065/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451065 Building REAL300024451066 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451066' /scratch/stefan/7786230/working/building/REAL300024451066 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451066 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451066/0 /scratch/stefan/7786230/working/building/REAL300024451066 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/981 `/scratch/stefan/7786230/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451066/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451066 none CC1C(NC(=O)C(F)=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 20, 20, 57, 76, 127, 127, 127, 127, 127, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 57, 57, 127] 127 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 330 number of broken/clashed sets: 18 ./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: REAL300024451066 none CC1C(NC(=O)C(F)=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 97, 97, 97, 127, 127, 127, 127, 127, 80, 80, 80, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 97, 127, 127, 127, 127, 127, 127, 80, 80, 80, 80, 80, 80, 40, 40, 1] 127 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 425 number of broken/clashed sets: 18 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451066 none CC1C(NC(=O)C(F)=C2CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 13, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 14, 29, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 14, 14, 80] 127 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451066 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451066 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451066/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451066 Building REAL300024451067 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451067' /scratch/stefan/7786230/working/building/REAL300024451067 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451067 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451067/0 /scratch/stefan/7786230/working/building/REAL300024451067 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/982 `/scratch/stefan/7786230/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451067/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451067 none CCC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 10, 10, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 30, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7] 30 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 64 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451067 none CCC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 5, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 7, 7, 7, 1, 1, 6, 6, 6, 6, 6, 5, 8, 8, 24, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 2, 2, 2] 30 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451067 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451067 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451067/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451067 Building REAL300024451068 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451068' /scratch/stefan/7786230/working/building/REAL300024451068 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451068 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451068/0 /scratch/stefan/7786230/working/building/REAL300024451068 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/983 `/scratch/stefan/7786230/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C(F)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451068/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451068 none CC1C(NC(=O)C(F)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 6, 6, 6, 6, 6, 6, 6, 6, 1] 18 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 30 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451068 none CC1C(NC(=O)C(F)C(C)(C)O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 15, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 5, 5, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 1, 1, 1, 1, 1, 1, 5, 5, 6] 18 rigid atoms, others: [0, 1, 2, 3, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451068 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451068 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451068/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451068 Building REAL300024451069 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451069' /scratch/stefan/7786230/working/building/REAL300024451069 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451069 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451069/0 /scratch/stefan/7786230/working/building/REAL300024451069 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/984 `/scratch/stefan/7786230/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451069/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451069 none CC(C)CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 158, 137, 122, 53, 53, 53, 41, 41, 41, 41, 41, 41, 22, 41, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 122, 122, 53, 41, 41, 41, 41, 41, 41, 41, 22, 22, 1, 41, 41, 41, 41] 201 rigid atoms, others: [50, 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, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 872 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451069 none CC(C)CCOCC(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 35, 26, 18, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 41, 41, 41, 41, 41, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 26, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 41, 1, 2, 2, 2] 201 rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 51, 46, 41, 25, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451069 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451069 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451069/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451069 Building REAL300024451070 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451070' /scratch/stefan/7786230/working/building/REAL300024451070 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451070 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451070/0 /scratch/stefan/7786230/working/building/REAL300024451070 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/985 `/scratch/stefan/7786230/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451070/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451070 none CC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 113, 201, 201, 113, 113, 66, 66, 66, 66, 66, 63, 49, 63, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 201, 201, 201, 201, 201, 201, 603, 113, 66, 66, 66, 66, 66, 66, 66, 49, 49, 1, 66, 66, 66, 66] 603 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 1393 number of broken/clashed sets: 239 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451070 none CC(CO)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 6, 27, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 66, 66, 66, 66, 66, 1, 1, 27, 27, 27, 27, 38, 38, 114, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 66, 1, 2, 2, 2] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45]) total number of confs: 382 number of broken/clashed sets: 239 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451070 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451070 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451070/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451070 Building REAL300024451071 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451071' /scratch/stefan/7786230/working/building/REAL300024451071 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451071 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451071/0 /scratch/stefan/7786230/working/building/REAL300024451071 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/986 `/scratch/stefan/7786230/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451071/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451071 none CC1C(NC(=O)C2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 51, 114, 201, 201, 201, 201, 201, 7, 7, 7, 7, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 51, 51, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 24 ./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: REAL300024451071 none CC1C(NC(=O)C2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [108, 108, 108, 108, 117, 117, 117, 201, 201, 201, 201, 108, 108, 108, 106, 51, 106, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 117, 201, 201, 108, 108, 108, 108, 108, 108, 51, 51, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 538 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451071 none CC1C(NC(=O)C2=CON=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 13, 37, 108, 108, 108, 108, 108, 2, 2, 2, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 108] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 11, 12, 34, 14, 13, 35, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451071 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451071 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451071/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451071 Building REAL300024451072 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451072' /scratch/stefan/7786230/working/building/REAL300024451072 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451072 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451072/0 /scratch/stefan/7786230/working/building/REAL300024451072 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/987 `/scratch/stefan/7786230/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451072/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451072 none CC1C(NC(=O)C=CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 24, 24, 7, 23, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 41, 41, 88, 124, 190, 190, 190, 190, 190, 29, 29, 29, 29, 29, 24, 7, 6, 1, 1, 1, 29, 29, 29, 29, 29, 29, 88, 88, 190] 190 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 504 number of broken/clashed sets: 27 ./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: REAL300024451072 none CC1C(NC(=O)C=CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 120, 120, 120, 175, 175, 190, 190, 190, 190, 112, 112, 112, 108, 40, 108, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 120, 175, 175, 190, 190, 190, 112, 112, 112, 112, 112, 112, 40, 40, 1] 190 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 587 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451072 none CC1C(NC(=O)C=CC2=CNC=N2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 15, 15, 29, 29, 29, 29, 1, 1, 1, 1, 1, 3, 3, 14, 32, 112, 112, 112, 112, 112, 2, 2, 2, 1, 1, 4, 15, 15, 29, 29, 29, 1, 1, 1, 1, 1, 1, 14, 14, 112] 190 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 241 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451072 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451072 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451072/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451072 Building REAL300024451073 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451073' /scratch/stefan/7786230/working/building/REAL300024451073 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451073 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451073/0 /scratch/stefan/7786230/working/building/REAL300024451073 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/988 `/scratch/stefan/7786230/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451073/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451073 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 12, 12, 7, 11, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 17, 17, 30, 40, 57, 57, 57, 57, 57, 13, 13, 13, 13, 13, 12, 7, 7, 1, 1, 1, 13, 13, 13, 13, 13, 13, 30, 30, 57] 57 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 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: REAL300024451073 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 17, 17, 17, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16, 15, 16, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 17, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 15, 15, 1] 20 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 2 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451073 none CC1C(NC(=O)C=CC2=NC=CN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 9, 9, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 6, 8, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 3, 9, 9, 11, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 16] 20 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451073 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451073 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451073/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451073 Building REAL300024451074 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451074' /scratch/stefan/7786230/working/building/REAL300024451074 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451074 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451074/0 /scratch/stefan/7786230/working/building/REAL300024451074 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/989 `/scratch/stefan/7786230/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1) `REAL300024451074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451074/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451074 none CCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 20, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 105, 105, 105, 105, 105, 1, 1, 20, 20, 20, 22, 22, 22, 22, 22, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 105, 1, 2, 2, 2, 20, 20, 20, 20] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 39, 12, 45, 11, 40, 22, 41, 23, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 249 number of broken/clashed sets: 25 ./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: REAL300024451074 none CCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 125, 125, 125, 105, 105, 105, 105, 105, 90, 28, 90, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 125, 105, 105, 105, 105, 105, 105, 105, 28, 28, 1, 105, 105, 105, 105, 201, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 734 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451074 none CCC1(CC(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 14, 14, 14, 20, 20, 20, 20, 20, 29, 29, 79, 129, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 14, 20, 20, 20, 20, 20, 20, 20, 79, 79, 201, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 547 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451074 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451074 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451074/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451074 Building REAL300024451075 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451075' /scratch/stefan/7786230/working/building/REAL300024451075 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451075 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451075/0 /scratch/stefan/7786230/working/building/REAL300024451075 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/990 `/scratch/stefan/7786230/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451075/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451075 none CC1C(NC(=O)C=CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 23, 23, 6, 23, 6, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 35, 35, 60, 78, 109, 109, 109, 109, 109, 29, 29, 29, 29, 29, 23, 6, 6, 1, 1, 1, 29, 29, 29, 29, 29, 29, 60, 60, 109] 109 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 308 number of broken/clashed sets: 14 ./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: REAL300024451075 none CC1C(NC(=O)C=CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 84, 84, 84, 125, 125, 125, 125, 125, 125, 69, 69, 69, 65, 40, 65, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 84, 125, 125, 125, 125, 125, 69, 69, 69, 69, 69, 69, 40, 40, 1] 125 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 417 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451075 none CC1C(NC(=O)C=CC2=CNN=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 18, 18, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 11, 19, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 5, 18, 18, 31, 31, 31, 1, 1, 1, 1, 1, 1, 11, 11, 69] 124 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451075 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451075 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451075/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451075 Building REAL300024451076 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451076' /scratch/stefan/7786230/working/building/REAL300024451076 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451076 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451076/0 /scratch/stefan/7786230/working/building/REAL300024451076 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/991 `/scratch/stefan/7786230/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2C[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451076/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451076 none CC1C(NC(=O)[C@@H]2C[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 6, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 9] 9 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 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, 44, 45]) total number of confs: 35 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: REAL300024451076 none CC1C(NC(=O)[C@@H]2C[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 1] 9 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 5 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451076 none CC1C(NC(=O)[C@@H]2C[C@H]2CF)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 9, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 3, 8, 8, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 5] 9 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451076 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451076 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451076/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451076 Building REAL300024451077 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451077' /scratch/stefan/7786230/working/building/REAL300024451077 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451077 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451077/0 /scratch/stefan/7786230/working/building/REAL300024451077 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/992 `/scratch/stefan/7786230/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@@H]2CCCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451077/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451077 none CC1C(NC(=O)[C@@H]2CCCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 24, 24, 56, 75, 126, 126, 126, 126, 126, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 17, 17, 56, 56, 126] 378 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 345 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: REAL300024451077 none CC1C(NC(=O)[C@@H]2CCCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 86, 86, 86, 126, 126, 126, 126, 126, 126, 126, 126, 66, 66, 66, 63, 35, 63, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 86, 126, 126, 126, 126, 126, 126, 126, 126, 378, 66, 66, 66, 66, 66, 66, 35, 35, 1] 378 rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 802 number of broken/clashed sets: 69 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451077 none CC1C(NC(=O)[C@@H]2CCCC[C@H]2O)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 12, 20, 66, 66, 66, 66, 66, 2, 2, 2, 1, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 51, 1, 1, 1, 1, 1, 1, 12, 12, 66] 378 rigid atoms, others: [0, 1, 2, 3, 48, 33, 32, 44, 45, 46, 15, 16, 17, 18, 19, 49, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451077 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451077 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451077/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451077 Building REAL300024451078 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451078' /scratch/stefan/7786230/working/building/REAL300024451078 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451078 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451078/0 /scratch/stefan/7786230/working/building/REAL300024451078 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/993 `/scratch/stefan/7786230/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(C)C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451078/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451078 none CC1C(NC(=O)C2(C)C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 51, 107, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 51, 51, 201] 201 rigid atoms, others: [43, 4, 37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 36, 38, 42, 39] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 438 number of broken/clashed sets: 22 ./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: REAL300024451078 none CC1C(NC(=O)C2(C)C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 98, 98, 99, 99, 99, 201, 201, 201, 201, 201, 201, 98, 98, 98, 95, 47, 95, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 47, 47, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 620 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451078 none CC1C(NC(=O)C2(C)C=CCCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 13, 33, 98, 98, 98, 98, 98, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 98] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451078 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451078 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451078/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451078 Building REAL300024451079 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451079' /scratch/stefan/7786230/working/building/REAL300024451079 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451079 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451079/0 /scratch/stefan/7786230/working/building/REAL300024451079 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/994 `/scratch/stefan/7786230/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451079/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451079 none CC1C(NC(=O)CC2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 55, 55, 95, 134, 201, 201, 201, 201, 201, 35, 35, 35, 35, 35, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 95, 95, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 43, 41, 39, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 569 number of broken/clashed sets: 8 ./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: REAL300024451079 none CC1C(NC(=O)CC2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 62, 62, 62, 68, 68, 68, 172, 201, 201, 201, 201, 201, 62, 62, 62, 57, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 68, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 62, 27, 27, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 782 number of broken/clashed sets: 8 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451079 none CC1C(NC(=O)CC2CC3(CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 3, 3, 9, 14, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 3, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 9, 9, 62] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451079 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451079 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451079/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451079 Building REAL300024451080 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451080' /scratch/stefan/7786230/working/building/REAL300024451080 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451080 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451080/0 /scratch/stefan/7786230/working/building/REAL300024451080 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/995 `/scratch/stefan/7786230/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1C) `REAL300024451080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451080/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451080 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 29, 120, 120, 120, 120, 120, 1, 1, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 120, 1, 2, 2, 2, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 25 ./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: REAL300024451080 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 125, 125, 125, 120, 120, 120, 120, 120, 117, 55, 117, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 125, 120, 120, 120, 120, 120, 120, 120, 55, 55, 1, 120, 120, 120, 120, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 540 number of broken/clashed sets: 25 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451080 none CC1=CC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 9, 9, 9, 9, 13, 13, 46, 100, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 2, 2, 2, 1, 5, 9, 9, 9, 9, 9, 9, 9, 46, 46, 201, 9, 9, 9, 9, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 433 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451080 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451080 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451080/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451080 Building REAL300024451081 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451081' /scratch/stefan/7786230/working/building/REAL300024451081 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451081 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451081/0 /scratch/stefan/7786230/working/building/REAL300024451081 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/996 `/scratch/stefan/7786230/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCOC1) `REAL300024451081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451081/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451081 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 138, 138, 138, 112, 112, 112, 112, 112, 99, 31, 99, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 112, 112, 112, 112, 112, 112, 112, 31, 31, 1, 112, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 762 number of broken/clashed sets: 29 ./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: REAL300024451081 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 10, 10, 10, 16, 16, 16, 16, 16, 26, 26, 78, 119, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 16, 16, 16, 16, 16, 16, 16, 78, 78, 201, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 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]) total number of confs: 515 number of broken/clashed sets: 29 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451081 none CC(C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 24, 112, 112, 112, 112, 112, 1, 1, 13, 16, 16, 16, 16, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 112, 1, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 21, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 230 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451081 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451081 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451081/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451081 Building REAL300024451082 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451082' /scratch/stefan/7786230/working/building/REAL300024451082 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451082 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451082/0 /scratch/stefan/7786230/working/building/REAL300024451082 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/997 `/scratch/stefan/7786230/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COC(Cl)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451082/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451082 none CC1C(NC(=O)C2=COC(Cl)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 54, 119, 201, 201, 201, 201, 201, 9, 9, 9, 9, 9, 5, 1, 1, 9, 9, 9, 9, 9, 9, 54, 54, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 440 number of broken/clashed sets: 24 ./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: REAL300024451082 none CC1C(NC(=O)C2=COC(Cl)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 129, 129, 129, 201, 201, 201, 201, 201, 116, 116, 116, 112, 52, 112, 13, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 129, 201, 201, 116, 116, 116, 116, 116, 116, 52, 52, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 551 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451082 none CC1C(NC(=O)C2=COC(Cl)=C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 13, 37, 116, 116, 116, 116, 116, 2, 2, 2, 1, 1, 3, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 116] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451082 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451082 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451082/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451082 Building REAL300024451083 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451083' /scratch/stefan/7786230/working/building/REAL300024451083 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451083 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451083/0 /scratch/stefan/7786230/working/building/REAL300024451083 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/998 `/scratch/stefan/7786230/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)[C@H]2C[C@H]([NH+](C)C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451083/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451083 none CC1C(NC(=O)[C@H]2C[C@H]([NH+](C)C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 19, 19, 19, 19, 19, 31, 31, 73, 92, 124, 124, 124, 124, 124, 19, 19, 19, 19, 19, 7, 1, 1, 2, 2, 2, 3, 3, 3, 1, 1, 19, 19, 19, 19, 19, 19, 73, 73, 124] 124 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 44, 45, 15, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 405 number of broken/clashed sets: 27 ./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: REAL300024451083 none CC1C(NC(=O)[C@H]2C[C@H]([NH+](C)C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 54, 54, 95, 95, 95, 124, 124, 124, 124, 124, 124, 124, 124, 124, 54, 54, 54, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 95, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 54, 54, 54, 54, 54, 54, 28, 28, 1] 124 rigid atoms, others: [54, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 430 number of broken/clashed sets: 27 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451083 none CC1C(NC(=O)[C@H]2C[C@H]([NH+](C)C)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 19, 19, 19, 19, 19, 29, 29, 29, 19, 1, 1, 1, 1, 1, 3, 3, 9, 16, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 6, 19, 19, 29, 29, 29, 29, 29, 29, 19, 19, 1, 1, 1, 1, 1, 1, 9, 9, 54] 124 rigid atoms, others: [0, 1, 2, 3, 48, 49, 51, 33, 34, 46, 47, 16, 17, 18, 19, 20, 50] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451083 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451083 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451083/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451083 Building REAL300024451084 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451084' /scratch/stefan/7786230/working/building/REAL300024451084 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451084 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451084/0 /scratch/stefan/7786230/working/building/REAL300024451084 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/999 `/scratch/stefan/7786230/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451084/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451084 none CC(CC[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 129, 191, 196, 201, 201, 201, 201, 129, 129, 77, 77, 77, 77, 77, 71, 29, 71, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 191, 191, 191, 191, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 129, 77, 77, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77, 77, 77] 201 rigid atoms, others: [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, 48, 49, 50, 51, 53, 54, 55, 56]) total number of confs: 781 number of broken/clashed sets: 200 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451084 none CC(CC[NH+](C)C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 18, 25, 29, 43, 42, 42, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 77, 77, 77, 77, 77, 1, 1, 18, 18, 18, 18, 26, 26, 28, 29, 43, 43, 43, 43, 43, 43, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 77, 1, 2, 2, 2] 201 rigid atoms, others: [16, 11, 15, 44, 10, 43, 12, 13, 14, 45, 48, 49, 46, 27, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52, 54, 55, 56]) total number of confs: 352 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451084 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451084 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451084/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451084 Building REAL300024451085 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451085' /scratch/stefan/7786230/working/building/REAL300024451085 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451085 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451085/0 /scratch/stefan/7786230/working/building/REAL300024451085 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1000 `/scratch/stefan/7786230/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CC(C3CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451085/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451085 none CC1C(NC(=O)C2CC(C3CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 16, 16, 16, 16, 16, 24, 24, 63, 104, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 16, 16, 16, 16, 16, 16, 63, 63, 201] 201 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 42, 43, 12, 36] set([0, 1, 2, 3, 5, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 480 number of broken/clashed sets: 47 ./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.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: REAL300024451085 none CC1C(NC(=O)C2CC(C3CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 58, 58, 63, 63, 63, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 36, 58, 13, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 36, 36, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 561 number of broken/clashed sets: 47 ./output.4.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: REAL300024451085 none CC1C(NC(=O)C2CC(C3CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 21, 18, 18, 4, 18, 4, 4, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 31, 31, 71, 111, 201, 201, 201, 201, 201, 21, 21, 21, 21, 21, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 21, 21, 21, 71, 71, 201] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 490 number of broken/clashed sets: 47 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451085 none CC1C(NC(=O)C2CC(C3CC3)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 21, 21, 16, 1, 1, 1, 1, 1, 3, 3, 9, 15, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 21, 21, 21, 21, 21, 16, 16, 1, 1, 1, 1, 1, 1, 9, 9, 58] 201 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451085 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451085 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451085/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451085 Building REAL300024451086 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451086' /scratch/stefan/7786230/working/building/REAL300024451086 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451086 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451086/0 /scratch/stefan/7786230/working/building/REAL300024451086 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1001 `/scratch/stefan/7786230/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451086/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451086 none CC(C)[C@H](NC=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5] 5 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 6 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451086 none CC(C)[C@H](NC=O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 3, 3, 3, 4, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 5, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 1, 2, 2, 2] 5 rigid atoms, others: [48, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 49, 50, 51]) total number of confs: 35 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451086 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451086 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451086/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451086 Building REAL300024451087 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451087' /scratch/stefan/7786230/working/building/REAL300024451087 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451087 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451087/0 /scratch/stefan/7786230/working/building/REAL300024451087 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1002 `/scratch/stefan/7786230/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024451087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451087/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451087 none CCSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 23, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 69, 69, 69, 69, 69, 1, 1, 13, 13, 25, 25, 25, 25, 25, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 69, 1, 2, 2, 2, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 14 ./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: REAL300024451087 none CCSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 87, 87, 87, 69, 69, 69, 69, 69, 62, 26, 62, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 175, 175, 201, 201, 201, 201, 201, 87, 69, 69, 69, 69, 69, 69, 69, 26, 26, 1, 69, 69, 69, 69, 175, 175, 175, 175] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 578 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451087 none CCSC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 13, 23, 23, 56, 91, 175, 175, 175, 175, 175, 13, 13, 1, 1, 8, 8, 8, 8, 8, 10, 13, 13, 13, 13, 13, 13, 13, 56, 56, 175, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 46, 47, 48, 49, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 429 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451087 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451087 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451087/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451087 Building REAL300024451088 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451088' /scratch/stefan/7786230/working/building/REAL300024451088 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451088 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451088/0 /scratch/stefan/7786230/working/building/REAL300024451088 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1003 `/scratch/stefan/7786230/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451088/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451088 none CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 81, 81, 81, 134, 134, 180, 180, 180, 180, 79, 79, 79, 77, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 81, 134, 134, 180, 180, 180, 180, 180, 180, 79, 79, 79, 79, 79, 79, 38, 38, 1] 180 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 589 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451088 none CC1C(NC(=O)C=CC(=O)N(C)C)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 10, 10, 27, 27, 27, 27, 1, 1, 1, 1, 1, 3, 3, 12, 25, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 3, 10, 10, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 12, 12, 79] 180 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 45, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451088 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451088 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451088/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451088 Building REAL300024451089 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451089' /scratch/stefan/7786230/working/building/REAL300024451089 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451089 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451089/0 /scratch/stefan/7786230/working/building/REAL300024451089 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1004 `/scratch/stefan/7786230/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024451089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451089/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451089 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 62, 62, 62, 62, 62, 1, 1, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 1, 2, 2, 2, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 23 ./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: REAL300024451089 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 62, 62, 62, 62, 62, 62, 62, 62, 61, 32, 61, 13, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 201, 201, 62, 62, 62, 62, 62, 62, 62, 62, 32, 32, 1, 62, 62, 62, 62, 201, 201, 201, 201] 201 rigid atoms, others: [36, 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 592 number of broken/clashed sets: 23 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451089 none C#CC1(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 11, 11, 11, 11, 11, 18, 18, 48, 91, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 48, 48, 201, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 432 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451089 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451089 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451089/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451089 Building REAL300024451090 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451090' /scratch/stefan/7786230/working/building/REAL300024451090 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451090 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451090/0 /scratch/stefan/7786230/working/building/REAL300024451090 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1005 `/scratch/stefan/7786230/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1) `REAL300024451090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451090/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451090 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 75, 75, 75, 75, 75, 1, 1, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 75, 1, 2, 2, 2, 9] 100 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 22 ./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: REAL300024451090 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 75, 75, 75, 75, 75, 70, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 100, 100, 100, 100, 100, 100, 75, 75, 75, 75, 75, 75, 75, 37, 37, 1, 75, 75, 75, 75, 100] 100 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43, 44]) total number of confs: 328 number of broken/clashed sets: 22 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451090 none CC1=NC(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 13, 13, 38, 56, 100, 100, 100, 100, 100, 9, 9, 1, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 38, 38, 100, 9, 9, 9, 9, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451090 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451090 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451090/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451090 Building REAL300024451091 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451091' /scratch/stefan/7786230/working/building/REAL300024451091 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451091 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451091/0 /scratch/stefan/7786230/working/building/REAL300024451091 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1006 `/scratch/stefan/7786230/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=COCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451091/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451091 none CC1C(NC(=O)C2=COCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 24, 24, 61, 122, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 10, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 61, 61, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 452 number of broken/clashed sets: 24 ./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: REAL300024451091 none CC1C(NC(=O)C2=COCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 137, 137, 137, 146, 146, 146, 201, 201, 201, 201, 137, 137, 137, 132, 56, 132, 13, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 146, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 137, 56, 56, 1] 201 rigid atoms, others: [44, 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, 43]) total number of confs: 551 number of broken/clashed sets: 24 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451091 none CC1C(NC(=O)C2=COCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 14, 14, 14, 14, 1, 1, 1, 1, 1, 3, 3, 15, 46, 137, 137, 137, 137, 137, 2, 2, 2, 1, 1, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 15, 15, 137] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 241 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451091 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451091 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451091/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451091 Building REAL300024451092 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451092' /scratch/stefan/7786230/working/building/REAL300024451092 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451092 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451092/0 /scratch/stefan/7786230/working/building/REAL300024451092 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1007 `/scratch/stefan/7786230/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451092/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451092 none CC1C(NC(=O)C2=CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 30, 30, 79, 104, 165, 165, 165, 165, 165, 22, 22, 22, 22, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 79, 79, 165] 165 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 463 number of broken/clashed sets: 31 ./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: REAL300024451092 none CC1C(NC(=O)C2=CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 98, 98, 98, 165, 165, 165, 165, 165, 71, 71, 71, 67, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 98, 165, 165, 165, 165, 165, 165, 165, 71, 71, 71, 71, 71, 71, 39, 39, 1] 165 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 429 number of broken/clashed sets: 31 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451092 none CC1C(NC(=O)C2=CCCSC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 5, 5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 3, 3, 13, 21, 71, 71, 71, 71, 71, 2, 2, 2, 1, 1, 6, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 13, 13, 71] 165 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451092 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451092 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451092/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451092 Building REAL300024451093 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451093' /scratch/stefan/7786230/working/building/REAL300024451093 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451093 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451093/0 /scratch/stefan/7786230/working/building/REAL300024451093 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1008 `/scratch/stefan/7786230/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451093/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451093 none C[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 166, 201, 201, 166, 166, 155, 155, 155, 155, 155, 146, 52, 146, 13, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 603, 166, 155, 155, 155, 155, 155, 155, 155, 52, 52, 1, 155, 155, 155, 155] 603 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] 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, 39, 40, 41, 42]) total number of confs: 1287 number of broken/clashed sets: 60 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451093 none C[C@H](O)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 3, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 45, 155, 155, 155, 155, 155, 1, 1, 13, 13, 13, 39, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 155, 1, 2, 2, 2] 603 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 36, 37, 38, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451093 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451093 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451093/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451093 Building REAL300024451094 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451094' /scratch/stefan/7786230/working/building/REAL300024451094 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451094 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451094/0 /scratch/stefan/7786230/working/building/REAL300024451094 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1009 `/scratch/stefan/7786230/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(F)=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451094/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451094 none CC1C(NC(=O)C2=CC(F)=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 15, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 53, 103, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 4, 1, 1, 11, 11, 11, 11, 11, 11, 53, 53, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 432 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: REAL300024451094 none CC1C(NC(=O)C2=CC(F)=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 15, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [173, 173, 173, 173, 195, 195, 195, 201, 201, 201, 201, 201, 173, 173, 173, 169, 68, 169, 13, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 195, 201, 201, 173, 173, 173, 173, 173, 173, 68, 68, 1] 201 rigid atoms, others: [42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 609 number of broken/clashed sets: 16 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451094 none CC1C(NC(=O)C2=CC(F)=NN2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 1, 1, 1, 15, 8, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 12, 42, 173, 173, 173, 173, 173, 2, 2, 2, 1, 1, 6, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 173] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 12, 13, 14, 15, 34, 35, 29, 30, 16] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40, 41, 42]) total number of confs: 275 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451094 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451094 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451094/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451094 Building REAL300024451095 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451095' /scratch/stefan/7786230/working/building/REAL300024451095 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451095 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451095/0 /scratch/stefan/7786230/working/building/REAL300024451095 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1010 `/scratch/stefan/7786230/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451095/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451095 none CC1C(NC(=O)C2C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 26, 26, 69, 116, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 69, 69, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 490 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: REAL300024451095 none CC1C(NC(=O)C2C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 97, 97, 97, 201, 201, 201, 201, 89, 89, 89, 87, 45, 87, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 97, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 45, 45, 1] 201 rigid atoms, others: [46, 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, 43, 44, 45]) total number of confs: 634 number of broken/clashed sets: 17 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451095 none CC1C(NC(=O)C2C=CCC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 12, 28, 89, 89, 89, 89, 89, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 12, 12, 89] 201 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 43, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451095 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451095 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451095/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451095 Building REAL300024451096 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451096' /scratch/stefan/7786230/working/building/REAL300024451096 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451096 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451096/0 /scratch/stefan/7786230/working/building/REAL300024451096 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1011 `/scratch/stefan/7786230/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2CCCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451096/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451096 none CC1C(NC(=O)C2CCCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 22, 22, 82, 122, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 16, 16, 16, 16, 16, 16, 82, 82, 201] 603 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 12, 11, 40, 43, 36, 38, 42] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 523 number of broken/clashed sets: 126 ./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: REAL300024451096 none CC1C(NC(=O)C2CCCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 79, 79, 81, 81, 81, 201, 201, 201, 201, 201, 201, 79, 79, 79, 74, 40, 74, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 81, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 79, 79, 79, 79, 79, 79, 40, 40, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 1212 number of broken/clashed sets: 126 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451096 none CC1C(NC(=O)C2CCCC(O)C2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 3, 3, 13, 26, 79, 79, 79, 79, 79, 2, 2, 2, 1, 1, 3, 16, 16, 16, 16, 16, 16, 16, 16, 48, 16, 16, 1, 1, 1, 1, 1, 1, 13, 13, 79] 603 rigid atoms, others: [0, 1, 2, 3, 17, 48, 47, 44, 13, 14, 45, 16, 49, 46, 15, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52]) total number of confs: 227 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451096 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451096 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451096/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451096 Building REAL300024451097 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451097' /scratch/stefan/7786230/working/building/REAL300024451097 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451097 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451097/0 /scratch/stefan/7786230/working/building/REAL300024451097 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1012 `/scratch/stefan/7786230/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1) `REAL300024451097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451097/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451097 none CC1CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 33, 108, 108, 108, 108, 108, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 108, 1, 2, 2, 2, 15, 15, 15, 15] 158 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 212 number of broken/clashed sets: 35 ./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: REAL300024451097 none CC1CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 112, 112, 112, 108, 108, 108, 108, 108, 97, 40, 97, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 158, 158, 158, 158, 158, 158, 158, 158, 158, 112, 108, 108, 108, 108, 108, 108, 108, 40, 40, 1, 108, 108, 108, 108, 158, 158, 158, 158] 158 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 426 number of broken/clashed sets: 35 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451097 none CC1CC=C(C(=O)NC2CCCN(C(=O)CSC3=NNC(=O)[N-]3)C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 19, 19, 70, 102, 158, 158, 158, 158, 158, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 70, 70, 158, 15, 15, 15, 15, 1, 1, 1, 1] 158 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 51, 52, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 412 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451097 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451097 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451097/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451097 Building REAL300024451098 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451098' /scratch/stefan/7786230/working/building/REAL300024451098 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451098 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451098/0 /scratch/stefan/7786230/working/building/REAL300024451098 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1013 `/scratch/stefan/7786230/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451098/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451098 none CC(O)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 10, 14, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 42, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8, 8, 8] 42 rigid atoms, others: [44, 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, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 94 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451098 none CC(O)C(C)C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 5, 8, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 8, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 24, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 2, 2, 2] 42 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 45, 40, 41, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451098 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451098 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451098/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451098 Building REAL300024451099 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451099' /scratch/stefan/7786230/working/building/REAL300024451099 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451099 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451099/0 /scratch/stefan/7786230/working/building/REAL300024451099 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1014 `/scratch/stefan/7786230/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451099/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451099 none CC1C(NC(=O)C2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 19, 19, 62, 122, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 8, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 62, 62, 201] 603 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 474 number of broken/clashed sets: 57 ./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: REAL300024451099 none CC1C(NC(=O)C2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [122, 122, 122, 122, 143, 143, 143, 201, 201, 201, 201, 201, 122, 122, 122, 118, 47, 118, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 143, 603, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 122, 47, 47, 1] 603 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 1273 number of broken/clashed sets: 57 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451099 none CC1C(NC(=O)C2(O)CCOC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 12, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 13, 35, 122, 122, 122, 122, 122, 2, 2, 2, 1, 1, 3, 36, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 122] 603 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 44, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451099 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451099 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451099/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451099 Building REAL300024451100 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451100' /scratch/stefan/7786230/working/building/REAL300024451100 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451100 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451100/0 /scratch/stefan/7786230/working/building/REAL300024451100 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1015 `/scratch/stefan/7786230/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)C2=CC(=O)N(C)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451100/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451100 none CC1C(NC(=O)C2=CC(=O)N(C)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 18, 24, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 3, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 18, 18, 42] 42 rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 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: REAL300024451100 none CC1C(NC(=O)C2=CC(=O)N(C)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 40, 40, 40, 42, 42, 42, 42, 42, 42, 37, 37, 37, 33, 26, 33, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 40, 42, 42, 42, 42, 37, 37, 37, 37, 37, 37, 26, 26, 1] 42 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451100 none CC1C(NC(=O)C2=CC(=O)N(C)[N-]2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 11, 1, 1, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 10, 16, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 37] 42 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451100 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451100 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451100/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451100 Building REAL300024451101 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451101' /scratch/stefan/7786230/working/building/REAL300024451101 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451101 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451101/0 /scratch/stefan/7786230/working/building/REAL300024451101 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1016 `/scratch/stefan/7786230/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451101/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451101 none C=C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 84, 84, 84, 84, 84, 1, 1, 17, 17, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 84, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 20 ./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: REAL300024451101 none C=C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 99, 99, 99, 84, 84, 84, 84, 84, 83, 42, 83, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 99, 84, 84, 84, 84, 84, 84, 84, 42, 42, 1, 84, 84, 84, 84] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] 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, 40, 41, 42, 43]) total number of confs: 625 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451101 none C=C1CC1C(=O)NC1CCCN(C(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 17, 27, 27, 67, 120, 201, 201, 201, 201, 201, 17, 17, 1, 1, 1, 1, 1, 12, 17, 17, 17, 17, 17, 17, 17, 67, 67, 201, 17, 17, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([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]) total number of confs: 491 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451101 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451101 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451101/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451101 Building REAL300024451102 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451102' /scratch/stefan/7786230/working/building/REAL300024451102 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451102 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451102/0 /scratch/stefan/7786230/working/building/REAL300024451102 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1017 `/scratch/stefan/7786230/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CC2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1) `REAL300024451102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451102/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451102 none CC1C(NC(=O)CC2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 27, 27, 5, 27, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 52, 52, 97, 137, 201, 201, 201, 201, 201, 32, 32, 32, 32, 32, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 97, 97, 201] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 573 number of broken/clashed sets: 14 ./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: REAL300024451102 none CC1C(NC(=O)CC2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 73, 73, 73, 78, 78, 78, 173, 201, 201, 201, 201, 73, 73, 73, 67, 27, 67, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 78, 173, 173, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 73, 27, 27, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 793 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451102 none CC1C(NC(=O)CC2CC=CC2)CCCN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.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, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 15, 32, 32, 32, 32, 1, 1, 1, 1, 1, 3, 3, 10, 17, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 3, 15, 15, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 10, 10, 73] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 12, 13, 14, 15, 16, 44, 46, 45, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451102 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451102 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451102/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451102 Building REAL300024451103 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451103' /scratch/stefan/7786230/working/building/REAL300024451103 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451103 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451103/0 /scratch/stefan/7786230/working/building/REAL300024451103 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1018 `/scratch/stefan/7786230/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC1) `REAL300024451103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451103/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451103 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 47, 47, 30, 47, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 110, 110, 151, 201, 201, 70, 70, 70, 70, 70, 47, 30, 30, 1, 70, 70, 70, 70, 70, 70, 151, 151, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 850 number of broken/clashed sets: 10 ./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: REAL300024451103 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 33, 33, 33, 92, 106, 201, 201, 201, 201, 201, 17, 17, 17, 14, 3, 14, 1, 1, 1, 1, 17, 17, 17, 17, 17, 33, 92, 92, 201, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 531 number of broken/clashed sets: 10 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451103 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 14, 18, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 3, 3, 13, 17, 17, 2, 2, 2, 1, 1, 6, 14, 14, 70, 1, 1, 1, 1, 1, 1, 13, 13, 17, 17, 17, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451103 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451103 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451103/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451103 Building REAL300024451104 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451104' /scratch/stefan/7786230/working/building/REAL300024451104 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451104 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451104/0 /scratch/stefan/7786230/working/building/REAL300024451104 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1019 `/scratch/stefan/7786230/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(C)F) `REAL300024451104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451104/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451104 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [106, 106, 71, 71, 34, 71, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 148, 148, 201, 201, 201, 106, 106, 106, 106, 106, 71, 34, 34, 1, 106, 106, 106, 106, 106, 106, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 839 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451104 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 26, 33, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 2, 2, 2, 1, 1, 6, 26, 26, 106, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451104 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451104 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451104/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451104 Building REAL300024451105 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451105' /scratch/stefan/7786230/working/building/REAL300024451105 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451105 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451105/0 /scratch/stefan/7786230/working/building/REAL300024451105 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1020 `/scratch/stefan/7786230/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(F)F) `REAL300024451105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451105/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451105 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 56, 56, 33, 56, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 107, 107, 184, 184, 184, 73, 73, 73, 73, 73, 56, 33, 33, 1, 73, 73, 73, 73, 73, 73, 184, 184, 184] 184 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 773 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451105 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 29, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 2, 2, 2, 1, 1, 6, 23, 23, 73, 1, 1, 1, 1, 1, 1, 11, 11, 11] 184 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451105 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451105 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451105/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451105 Building REAL300024451106 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451106' /scratch/stefan/7786230/working/building/REAL300024451106 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451106 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451106/0 /scratch/stefan/7786230/working/building/REAL300024451106 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1021 `/scratch/stefan/7786230/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451106/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451106 none COCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 121, 82, 121, 82, 82, 82, 82, 57, 57, 31, 57, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 201, 201, 201, 82, 82, 82, 82, 82, 82, 82, 57, 31, 31, 1, 82, 82, 82, 82] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42]) total number of confs: 861 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451106 none COCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 19, 82, 82, 82, 82, 82, 1, 1, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 82, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 39, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451106 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451106 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451106/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451106 Building REAL300024451107 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451107' /scratch/stefan/7786230/working/building/REAL300024451107 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451107 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451107/0 /scratch/stefan/7786230/working/building/REAL300024451107 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1022 `/scratch/stefan/7786230/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=N1) `REAL300024451107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451107/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451107 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [151, 151, 138, 138, 59, 138, 13, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 181, 181, 182, 182, 182, 182, 182, 151, 151, 151, 151, 151, 138, 59, 59, 1, 151, 151, 151, 151, 151, 151, 182, 182, 182, 182] 182 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 590 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: REAL300024451107 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [6, 6, 6, 6, 10, 10, 10, 38, 103, 182, 182, 182, 182, 182, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 38, 38, 182, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 182 rigid atoms, others: [41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 365 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451107 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [1, 1, 1, 1, 4, 4, 4, 17, 59, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 4, 17, 17, 151, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 182 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451107 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451107 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451107/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451107 Building REAL300024451108 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451108' /scratch/stefan/7786230/working/building/REAL300024451108 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451108 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451108/0 /scratch/stefan/7786230/working/building/REAL300024451108 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1023 `/scratch/stefan/7786230/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1) `REAL300024451108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451108/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451108 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 132, 132, 59, 132, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 132, 59, 59, 1, 160, 160, 160, 160, 160, 160, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 675 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: REAL300024451108 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 14, 14, 14, 61, 113, 201, 201, 201, 201, 201, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 14, 61, 61, 201, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 436 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451108 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 32, 65, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 3, 3, 6, 6, 4, 6, 6, 2, 2, 2, 1, 1, 6, 32, 32, 160, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451108 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451108 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451108/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451108 Building REAL300024451109 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451109' /scratch/stefan/7786230/working/building/REAL300024451109 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451109 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451109/0 /scratch/stefan/7786230/working/building/REAL300024451109 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1024 `/scratch/stefan/7786230/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)C=C1) `REAL300024451109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451109/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451109 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [160, 160, 135, 135, 57, 135, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 135, 57, 57, 1, 160, 160, 160, 160, 160, 160, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 669 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: REAL300024451109 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 14, 14, 14, 55, 113, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 55, 55, 201, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 419 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451109 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 30, 66, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 6, 30, 30, 160, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 308 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451109 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451109 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451109/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451109 Building REAL300024451110 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451110' /scratch/stefan/7786230/working/building/REAL300024451110 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451110 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451110/0 /scratch/stefan/7786230/working/building/REAL300024451110 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1025 `/scratch/stefan/7786230/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451110/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451110 none CCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 88, 140, 88, 88, 88, 88, 58, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 88, 88, 88, 58, 31, 31, 1, 88, 88, 88, 88] 201 rigid atoms, others: [40, 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, 41, 42, 43, 44]) total number of confs: 831 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451110 none CCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 19, 88, 88, 88, 88, 88, 1, 1, 16, 16, 16, 16, 16, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 88, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 35, 21, 22, 41, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451110 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451110 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451110/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451110 Building REAL300024451111 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451111' /scratch/stefan/7786230/working/building/REAL300024451111 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451111 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451111/0 /scratch/stefan/7786230/working/building/REAL300024451111 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1026 `/scratch/stefan/7786230/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1) `REAL300024451111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451111/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451111 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [90, 90, 74, 74, 36, 74, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 120, 120, 201, 201, 201, 201, 201, 90, 90, 90, 90, 90, 74, 36, 36, 1, 90, 90, 90, 90, 90, 90, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 580 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: REAL300024451111 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 9, 9, 9, 21, 21, 21, 76, 102, 201, 201, 201, 201, 201, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 21, 76, 76, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 460 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451111 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 6, 6, 6, 22, 35, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 6, 22, 22, 90, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451111 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451111 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451111/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451111 Building REAL300024451112 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451112' /scratch/stefan/7786230/working/building/REAL300024451112 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451112 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451112/0 /scratch/stefan/7786230/working/building/REAL300024451112 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1027 `/scratch/stefan/7786230/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CS1) `REAL300024451112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451112/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451112 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 60, 39, 39, 26, 39, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 92, 92, 134, 201, 201, 201, 201, 60, 60, 60, 60, 60, 39, 26, 26, 1, 60, 60, 60, 60, 60, 60, 134, 134, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 709 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: REAL300024451112 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 39, 39, 39, 108, 116, 201, 201, 201, 201, 201, 22, 22, 22, 15, 4, 15, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 39, 108, 108, 201, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 584 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451112 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 11, 13, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 3, 3, 13, 22, 22, 22, 22, 2, 2, 2, 1, 1, 3, 11, 11, 60, 1, 1, 1, 1, 1, 1, 13, 13, 22, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451112 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451112 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451112/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451112 Building REAL300024451113 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451113' /scratch/stefan/7786230/working/building/REAL300024451113 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451113 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451113/0 /scratch/stefan/7786230/working/building/REAL300024451113 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1028 `/scratch/stefan/7786230/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CO1) `REAL300024451113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451113/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451113 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 46, 46, 31, 46, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 66, 66, 73, 73, 73, 73, 59, 59, 59, 59, 59, 46, 31, 31, 1, 59, 59, 59, 59, 59, 59, 73, 73, 73] 73 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 251 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: REAL300024451113 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 18, 18, 18, 52, 58, 73, 73, 73, 73, 73, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 18, 52, 52, 73, 10, 10, 10, 10, 10, 10, 1, 1, 1] 73 rigid atoms, others: [40, 41, 42, 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: 229 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451113 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 16, 24, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 2, 2, 2, 1, 1, 4, 16, 16, 59, 1, 1, 1, 1, 1, 1, 10, 10, 10] 73 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451113 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451113 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451113/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451113 Building REAL300024451114 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451114' /scratch/stefan/7786230/working/building/REAL300024451114 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451114 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451114/0 /scratch/stefan/7786230/working/building/REAL300024451114 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1029 `/scratch/stefan/7786230/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451114/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451114 none CC(=O)NCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 197, 132, 88, 132, 88, 88, 88, 88, 55, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 197, 197, 88, 88, 88, 88, 88, 88, 88, 55, 30, 30, 1, 88, 88, 88, 88] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 823 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451114 none CC(=O)NCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 32, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 22, 88, 88, 88, 88, 88, 1, 1, 32, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 88, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 42, 23, 24, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 254 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451114 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451114 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451114/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451114 Building REAL300024451115 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451115' /scratch/stefan/7786230/working/building/REAL300024451115 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451115 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451115/0 /scratch/stefan/7786230/working/building/REAL300024451115 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1030 `/scratch/stefan/7786230/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)SC=C1) `REAL300024451115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451115/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451115 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)SC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 52, 142, 142, 142, 142, 142, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 142, 1, 2, 2, 2, 9, 9] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 40, 35, 21, 22, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 252 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: REAL300024451115 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)SC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 142, 177, 142, 142, 142, 142, 125, 125, 54, 125, 13, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 142, 142, 125, 54, 54, 1, 142, 142, 142, 142, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 636 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451115 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)SC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 9, 9, 9, 9, 9, 14, 14, 14, 56, 106, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 14, 56, 56, 201, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451115 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451115 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451115/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451115 Building REAL300024451116 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451116' /scratch/stefan/7786230/working/building/REAL300024451116 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451116 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451116/0 /scratch/stefan/7786230/working/building/REAL300024451116 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1031 `/scratch/stefan/7786230/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)S1) `REAL300024451116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451116/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451116 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 38, 117, 117, 117, 117, 117, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 117, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 42, 23, 24, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 222 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: REAL300024451116 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 117, 146, 117, 117, 117, 117, 86, 86, 45, 86, 13, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 117, 117, 86, 45, 45, 1, 117, 117, 117, 117] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 620 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451116 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 80, 114, 201, 201, 201, 201, 201, 7, 7, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 19, 80, 80, 201, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451116 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451116 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451116/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451116 Building REAL300024451117 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451117' /scratch/stefan/7786230/working/building/REAL300024451117 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451117 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451117/0 /scratch/stefan/7786230/working/building/REAL300024451117 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1032 `/scratch/stefan/7786230/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CC=CO1) `REAL300024451117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451117/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451117 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 81, 81, 49, 81, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 123, 123, 172, 172, 201, 201, 201, 201, 100, 100, 100, 100, 100, 81, 49, 49, 1, 100, 100, 100, 100, 100, 100, 172, 172, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 665 number of broken/clashed sets: 6 ./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: REAL300024451117 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 67, 67, 67, 118, 136, 201, 201, 201, 201, 201, 44, 44, 44, 35, 10, 35, 10, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 67, 118, 118, 201, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 558 number of broken/clashed sets: 6 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451117 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C=CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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 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, 4, 4, 4, 17, 32, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 4, 4, 16, 16, 44, 44, 44, 44, 2, 2, 2, 1, 1, 4, 17, 17, 100, 1, 1, 1, 1, 1, 1, 16, 16, 44, 44, 44] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 248 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451117 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451117 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451117/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451117 Building REAL300024451118 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451118' /scratch/stefan/7786230/working/building/REAL300024451118 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451118 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451118/0 /scratch/stefan/7786230/working/building/REAL300024451118 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1033 `/scratch/stefan/7786230/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1F) `REAL300024451118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451118/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451118 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 101, 81, 81, 42, 81, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 149, 149, 201, 201, 201, 201, 201, 201, 101, 101, 101, 101, 101, 81, 42, 42, 1, 101, 101, 101, 101, 101, 101, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 629 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: REAL300024451118 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 19, 19, 19, 69, 109, 201, 201, 201, 201, 201, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 19, 69, 69, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 451 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451118 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 20, 33, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 3, 3, 9, 9, 5, 9, 9, 9, 2, 2, 2, 1, 1, 6, 20, 20, 101, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451118 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451118 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451118/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451118 Building REAL300024451119 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451119' /scratch/stefan/7786230/working/building/REAL300024451119 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451119 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451119/0 /scratch/stefan/7786230/working/building/REAL300024451119 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1034 `/scratch/stefan/7786230/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1) `REAL300024451119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451119/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451119 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [153, 153, 129, 129, 59, 129, 13, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 129, 59, 59, 1, 153, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 692 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: REAL300024451119 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 14, 14, 14, 60, 114, 201, 201, 201, 201, 201, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 14, 60, 60, 201, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 432 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451119 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 31, 63, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 3, 3, 6, 6, 4, 6, 6, 2, 2, 2, 1, 1, 6, 31, 31, 153, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451119 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451119 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451119/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451119 Building REAL300024451120 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451120' /scratch/stefan/7786230/working/building/REAL300024451120 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451120 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451120/0 /scratch/stefan/7786230/working/building/REAL300024451120 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1035 `/scratch/stefan/7786230/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451120/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451120 none CC(C)CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 141, 109, 141, 109, 109, 109, 109, 80, 80, 48, 80, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 109, 109, 109, 80, 48, 48, 1, 109, 109, 109, 109] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] 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, 44, 45, 46, 47]) total number of confs: 860 number of broken/clashed sets: 81 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451120 none CC(C)CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 37, 109, 109, 109, 109, 109, 1, 1, 12, 12, 12, 12, 12, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 109, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 44, 22, 23, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 247 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451120 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451120 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451120/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451120 Building REAL300024451121 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451121' /scratch/stefan/7786230/working/building/REAL300024451121 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451121 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451121/0 /scratch/stefan/7786230/working/building/REAL300024451121 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1036 `/scratch/stefan/7786230/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1) `REAL300024451121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451121/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451121 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [120, 120, 110, 110, 58, 110, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 143, 143, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 110, 58, 58, 1, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 715 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: REAL300024451121 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 11, 11, 11, 46, 105, 201, 201, 201, 201, 201, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 46, 46, 201, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 420 number of broken/clashed sets: 49 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451121 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 14, 41, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 3, 14, 14, 120, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451121 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451121 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451121/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451121 Building REAL300024451122 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451122' /scratch/stefan/7786230/working/building/REAL300024451122 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451122 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451122/0 /scratch/stefan/7786230/working/building/REAL300024451122 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1037 `/scratch/stefan/7786230/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC=N1) `REAL300024451122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451122/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451122 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 127, 127, 61, 127, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 196, 196, 196, 196, 196, 196, 196, 146, 146, 146, 146, 146, 127, 61, 61, 1, 146, 146, 146, 146, 146, 146, 196, 196, 196] 196 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 670 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: REAL300024451122 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 10, 10, 10, 46, 106, 196, 196, 196, 196, 196, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 46, 46, 196, 4, 4, 4, 4, 4, 4, 1, 1, 1] 196 rigid atoms, others: [41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 393 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451122 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 28, 63, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 6, 28, 28, 146, 1, 1, 1, 1, 1, 1, 4, 4, 4] 196 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451122 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451122 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451122/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451122 Building REAL300024451123 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451123' /scratch/stefan/7786230/working/building/REAL300024451123 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451123 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451123/0 /scratch/stefan/7786230/working/building/REAL300024451123 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1038 `/scratch/stefan/7786230/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451123/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451123 none CC1=CC=CC=C1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 6, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 48, 146, 146, 146, 146, 146, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 146, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 45, 25, 26, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 262 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: REAL300024451123 none CC1=CC=CC=C1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 178, 146, 178, 146, 146, 146, 146, 135, 135, 64, 135, 13, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 146, 146, 135, 64, 64, 1, 146, 146, 146, 146] 201 rigid atoms, others: [44, 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, 43, 45, 46, 47, 48]) total number of confs: 629 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451123 none CC1=CC=CC=C1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 8, 8, 8, 8, 8, 12, 12, 12, 50, 106, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 12, 50, 50, 201, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 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, 48]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451123 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451123 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451123/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451123 Building REAL300024451124 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451124' /scratch/stefan/7786230/working/building/REAL300024451124 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451124 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451124/0 /scratch/stefan/7786230/working/building/REAL300024451124 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1039 `/scratch/stefan/7786230/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCC1) `REAL300024451124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451124/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451124 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [100, 100, 77, 77, 48, 77, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 120, 120, 157, 201, 201, 201, 201, 100, 100, 100, 100, 100, 77, 48, 48, 1, 100, 100, 100, 100, 100, 100, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 808 number of broken/clashed sets: 20 ./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: REAL300024451124 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 34, 34, 34, 101, 119, 201, 201, 201, 201, 201, 23, 23, 23, 17, 5, 17, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 34, 101, 101, 201, 23, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 547 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451124 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 16, 31, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 4, 4, 12, 23, 23, 23, 23, 2, 2, 2, 1, 1, 4, 16, 16, 100, 1, 1, 1, 1, 1, 1, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 249 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451124 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451124 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451124/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451124 Building REAL300024451125 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451125' /scratch/stefan/7786230/working/building/REAL300024451125 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451125 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451125/0 /scratch/stefan/7786230/working/building/REAL300024451125 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1040 `/scratch/stefan/7786230/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1CCCC1) `REAL300024451125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451125/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451125 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 59, 40, 40, 27, 40, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 82, 82, 119, 144, 201, 201, 201, 201, 59, 59, 59, 59, 59, 40, 27, 27, 1, 59, 59, 59, 59, 59, 59, 119, 119, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 859 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: REAL300024451125 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 42, 42, 42, 111, 118, 201, 201, 201, 201, 201, 25, 25, 25, 22, 7, 22, 5, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 42, 111, 111, 201, 25, 25, 25, 25, 25, 25, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 595 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451125 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CCC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 12, 14, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 3, 3, 9, 12, 25, 25, 25, 25, 2, 2, 2, 1, 1, 4, 12, 12, 59, 1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451125 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451125 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451125/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451125 Building REAL300024451126 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451126' /scratch/stefan/7786230/working/building/REAL300024451126 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451126 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451126/0 /scratch/stefan/7786230/working/building/REAL300024451126 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1041 `/scratch/stefan/7786230/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(F)=C1) `REAL300024451126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451126/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451126 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 92, 72, 72, 36, 72, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 131, 131, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 92, 72, 36, 36, 1, 92, 92, 92, 92, 92, 92, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 598 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: REAL300024451126 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 20, 20, 20, 76, 102, 201, 201, 201, 201, 201, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 20, 76, 76, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 465 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451126 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 22, 32, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 6, 22, 22, 92, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451126 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451126 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451126/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451126 Building REAL300024451127 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451127' /scratch/stefan/7786230/working/building/REAL300024451127 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451127 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451127/0 /scratch/stefan/7786230/working/building/REAL300024451127 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1042 `/scratch/stefan/7786230/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CS1) `REAL300024451127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451127/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451127 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 101, 69, 69, 40, 69, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 128, 128, 201, 201, 201, 201, 101, 101, 101, 101, 101, 69, 40, 40, 1, 101, 101, 101, 101, 101, 101, 201, 201, 201] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 597 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: REAL300024451127 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 25, 25, 25, 84, 102, 201, 201, 201, 201, 201, 11, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 25, 84, 84, 201, 11, 11, 11, 11, 11, 11, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 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: 492 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451127 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 25, 37, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 2, 2, 2, 1, 1, 6, 25, 25, 101, 1, 1, 1, 1, 1, 1, 11, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451127 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451127 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451127/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451127 Building REAL300024451128 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451128' /scratch/stefan/7786230/working/building/REAL300024451128 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451128 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451128/0 /scratch/stefan/7786230/working/building/REAL300024451128 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1043 `/scratch/stefan/7786230/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1) `REAL300024451128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451128/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451128 none CC1=CN=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 67, 160, 160, 160, 160, 160, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 160, 1, 2, 2, 2, 5] 183 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 42, 23, 24, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 279 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: REAL300024451128 none CC1=CN=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [183, 183, 183, 183, 182, 160, 182, 160, 160, 160, 160, 149, 149, 62, 149, 13, 1, 1, 1, 1, 1, 1, 1, 160, 160, 183, 183, 183, 183, 183, 183, 160, 160, 160, 160, 160, 160, 160, 149, 62, 62, 1, 160, 160, 160, 160, 183] 183 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 587 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451128 none CC1=CN=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 36, 100, 183, 183, 183, 183, 183, 5, 5, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 8, 36, 36, 183, 5, 5, 5, 5, 1] 183 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 360 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451128 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451128 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451128/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451128 Building REAL300024451129 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451129' /scratch/stefan/7786230/working/building/REAL300024451129 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451129 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451129/0 /scratch/stefan/7786230/working/building/REAL300024451129 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1044 `/scratch/stefan/7786230/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSC=C1) `REAL300024451129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451129/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451129 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 59, 38, 38, 26, 38, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 83, 83, 106, 201, 201, 201, 201, 59, 59, 59, 59, 59, 38, 26, 26, 1, 59, 59, 59, 59, 59, 59, 106, 106, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 623 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: REAL300024451129 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 37, 37, 37, 103, 112, 201, 201, 201, 201, 201, 20, 20, 20, 13, 3, 13, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 37, 103, 103, 201, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 564 number of broken/clashed sets: 45 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451129 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 11, 13, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 3, 3, 11, 20, 20, 20, 20, 2, 2, 2, 1, 1, 4, 11, 11, 59, 1, 1, 1, 1, 1, 1, 11, 11, 20, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451129 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451129 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451129/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451129 Building REAL300024451130 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451130' /scratch/stefan/7786230/working/building/REAL300024451130 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451130 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451130/0 /scratch/stefan/7786230/working/building/REAL300024451130 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1045 `/scratch/stefan/7786230/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451130/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451130 none CC1CC1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 43, 98, 98, 98, 98, 98, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 98, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 22, 23, 36, 42, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 208 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: REAL300024451130 none CC1CC1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 147, 98, 147, 98, 98, 98, 98, 79, 79, 47, 79, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 98, 98, 98, 98, 79, 47, 47, 1, 98, 98, 98, 98] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 736 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451130 none CC1CC1C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 61, 105, 201, 201, 201, 201, 201, 4, 4, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 15, 61, 61, 201, 4, 4, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 27, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451130 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451130 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451130/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451130 Building REAL300024451131 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451131' /scratch/stefan/7786230/working/building/REAL300024451131 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451131 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451131/0 /scratch/stefan/7786230/working/building/REAL300024451131 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1046 `/scratch/stefan/7786230/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=C1) `REAL300024451131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451131/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451131 none CC1=CC=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 5, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 30, 91, 91, 91, 91, 91, 1, 1, 9, 9, 9, 9, 7, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 91, 1, 2, 2, 2, 9] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 24, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 205 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: REAL300024451131 none CC1=CC=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 127, 91, 127, 91, 91, 91, 91, 71, 71, 37, 71, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 91, 71, 37, 37, 1, 91, 91, 91, 91, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 594 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451131 none CC1=CC=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 22, 22, 22, 78, 102, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 22, 78, 78, 201, 9, 9, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 468 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451131 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451131 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451131/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451131 Building REAL300024451132 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451132' /scratch/stefan/7786230/working/building/REAL300024451132 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451132 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451132/0 /scratch/stefan/7786230/working/building/REAL300024451132 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1047 `/scratch/stefan/7786230/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451132/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451132 none CCOCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 97, 65, 97, 65, 65, 65, 65, 45, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 180, 180, 65, 65, 65, 65, 65, 65, 65, 45, 29, 29, 1, 65, 65, 65, 65] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 814 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451132 none CCOCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 26, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 16, 65, 65, 65, 65, 65, 1, 1, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 65, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 22, 23, 36, 42, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451132 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451132 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451132/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451132 Building REAL300024451133 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451133' /scratch/stefan/7786230/working/building/REAL300024451133 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451133 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451133/0 /scratch/stefan/7786230/working/building/REAL300024451133 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1048 `/scratch/stefan/7786230/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451133/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451133 none CC(C)=CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 161, 136, 161, 136, 136, 136, 136, 123, 123, 63, 123, 13, 1, 1, 1, 1, 1, 1, 1, 136, 136, 189, 189, 189, 189, 189, 189, 189, 136, 136, 136, 136, 136, 136, 136, 123, 63, 63, 1, 136, 136, 136, 136] 189 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 660 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451133 none CC(C)=CC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 47, 136, 136, 136, 136, 136, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 136, 1, 2, 2, 2] 189 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 22, 23, 36, 42, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451133 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451133 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451133/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451133 Building REAL300024451134 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451134' /scratch/stefan/7786230/working/building/REAL300024451134 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451134 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451134/0 /scratch/stefan/7786230/working/building/REAL300024451134 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1049 `/scratch/stefan/7786230/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCCO1) `REAL300024451134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451134/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451134 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 145, 116, 116, 55, 116, 13, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 189, 189, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 116, 55, 55, 1, 145, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 680 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: REAL300024451134 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 16, 16, 16, 66, 116, 201, 201, 201, 201, 201, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 16, 66, 66, 201, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 455 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451134 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 28, 57, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 6, 28, 28, 145, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451134 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451134 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451134/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451134 Building REAL300024451135 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451135' /scratch/stefan/7786230/working/building/REAL300024451135 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451135 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451135/0 /scratch/stefan/7786230/working/building/REAL300024451135 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1050 `/scratch/stefan/7786230/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=[N+]([O-])C=C1) `REAL300024451135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451135/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451135 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=[N+]([O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 119, 119, 54, 119, 13, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 188, 188, 188, 188, 188, 188, 188, 188, 148, 148, 148, 148, 148, 119, 54, 54, 1, 148, 148, 148, 148, 148, 148, 188, 188, 188, 188] 188 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 646 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: REAL300024451135 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=[N+]([O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 13, 13, 13, 54, 99, 188, 188, 188, 188, 188, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 13, 54, 54, 188, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 188 rigid atoms, others: [42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 403 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451135 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CC=[N+]([O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 31, 61, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 3, 3, 5, 5, 3, 3, 5, 5, 2, 2, 2, 1, 1, 6, 31, 31, 148, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 188 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 302 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451135 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451135 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451135/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451135 Building REAL300024451136 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451136' /scratch/stefan/7786230/working/building/REAL300024451136 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451136 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451136/0 /scratch/stefan/7786230/working/building/REAL300024451136 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1051 `/scratch/stefan/7786230/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC2C=CC1C2) `REAL300024451136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451136/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451136 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC2C=CC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [122, 122, 111, 111, 58, 111, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 152, 152, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 111, 58, 58, 1, 122, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 719 number of broken/clashed sets: 42 ./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: REAL300024451136 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC2C=CC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 10, 10, 10, 49, 104, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 49, 49, 201, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 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: 42 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451136 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CC2C=CC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 14, 42, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 3, 14, 14, 122, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451136 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451136 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451136/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451136 Building REAL300024451137 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451137' /scratch/stefan/7786230/working/building/REAL300024451137 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451137 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451137/0 /scratch/stefan/7786230/working/building/REAL300024451137 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1052 `/scratch/stefan/7786230/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451137/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451137 none CC(=O)NC(C)C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 132, 201, 93, 132, 93, 93, 93, 93, 59, 59, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 93, 93, 59, 31, 31, 1, 93, 93, 93, 93] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 853 number of broken/clashed sets: 58 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451137 none CC(=O)NC(C)C(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 25, 93, 93, 93, 93, 93, 1, 1, 18, 18, 18, 18, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 93, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 45, 40, 24, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451137 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451137 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451137/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451137 Building REAL300024451138 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451138' /scratch/stefan/7786230/working/building/REAL300024451138 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451138 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451138/0 /scratch/stefan/7786230/working/building/REAL300024451138 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1053 `/scratch/stefan/7786230/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC(=O)C=C1) `REAL300024451138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451138/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451138 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC(=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [122, 122, 91, 91, 42, 91, 13, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 162, 162, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 91, 42, 42, 1, 122, 122, 122, 122, 122, 122, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 641 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: REAL300024451138 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC(=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [8, 8, 8, 8, 19, 19, 19, 74, 114, 201, 201, 201, 201, 201, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 19, 74, 74, 201, 8, 8, 8, 8, 8, 8, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 18, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 478 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451138 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=NNC(=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 5, 5, 5, 20, 37, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 1, 5, 20, 20, 122, 1, 1, 1, 1, 1, 1, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451138 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451138 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451138/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451138 Building REAL300024451139 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451139' /scratch/stefan/7786230/working/building/REAL300024451139 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451139 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451139/0 /scratch/stefan/7786230/working/building/REAL300024451139 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1054 `/scratch/stefan/7786230/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)O1) `REAL300024451139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451139/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451139 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 60, 150, 150, 150, 150, 150, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 150, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 42, 23, 24, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 296 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: REAL300024451139 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 150, 201, 150, 150, 150, 150, 122, 122, 55, 122, 13, 1, 1, 1, 1, 1, 1, 1, 150, 150, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 150, 150, 122, 55, 55, 1, 150, 150, 150, 150] 201 rigid atoms, others: [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, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 690 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451139 none CC1=CC=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 6, 6, 6, 6, 6, 16, 16, 16, 61, 118, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 16, 61, 61, 201, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451139 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451139 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451139/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451139 Building REAL300024451140 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451140' /scratch/stefan/7786230/working/building/REAL300024451140 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451140 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451140/0 /scratch/stefan/7786230/working/building/REAL300024451140 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1055 `/scratch/stefan/7786230/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCCC1) `REAL300024451140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451140/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451140 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 66, 40, 40, 26, 40, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 104, 104, 159, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 40, 26, 26, 1, 66, 66, 66, 66, 66, 66, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 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, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 832 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: REAL300024451140 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 41, 41, 41, 108, 116, 201, 201, 201, 201, 201, 25, 25, 25, 20, 5, 20, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 41, 108, 108, 201, 25, 25, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [54, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 577 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451140 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 13, 15, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 3, 3, 13, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 4, 13, 13, 66, 1, 1, 1, 1, 1, 1, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451140 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451140 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451140/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451140 Building REAL300024451141 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451141' /scratch/stefan/7786230/working/building/REAL300024451141 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451141 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451141/0 /scratch/stefan/7786230/working/building/REAL300024451141 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1056 `/scratch/stefan/7786230/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCO1) `REAL300024451141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451141/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451141 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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: [100, 100, 71, 71, 34, 71, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 135, 135, 201, 201, 201, 201, 100, 100, 100, 100, 100, 71, 34, 34, 1, 100, 100, 100, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 721 number of broken/clashed sets: 20 ./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: REAL300024451141 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 10, 10, 10, 27, 27, 27, 90, 107, 201, 201, 201, 201, 201, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 27, 90, 90, 201, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 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: 508 number of broken/clashed sets: 20 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451141 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 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, 6, 6, 6, 22, 28, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 2, 2, 2, 1, 1, 6, 22, 22, 100, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 211 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451141 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451141 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451141/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451141 Building REAL300024451142 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451142' /scratch/stefan/7786230/working/building/REAL300024451142 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451142 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451142/0 /scratch/stefan/7786230/working/building/REAL300024451142 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1057 `/scratch/stefan/7786230/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451142/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451142 none CSCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 179, 116, 73, 116, 73, 73, 73, 73, 49, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 179, 179, 73, 73, 73, 73, 73, 73, 73, 49, 30, 30, 1, 73, 73, 73, 73] 201 rigid atoms, others: [38, 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, 39, 40, 41, 42]) total number of confs: 814 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451142 none CSCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 16, 73, 73, 73, 73, 73, 1, 1, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 73, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 39, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451142 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451142 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451142/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451142 Building REAL300024451143 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451143' /scratch/stefan/7786230/working/building/REAL300024451143 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451143 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451143/0 /scratch/stefan/7786230/working/building/REAL300024451143 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1058 `/scratch/stefan/7786230/working/3D/1058' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1) `REAL300024451143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451143/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451143 none CC1=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 44, 84, 84, 84, 84, 84, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 84, 1, 2, 2, 2] 90 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 41, 22, 23, 36, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 172 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: REAL300024451143 none CC1=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [90, 90, 90, 89, 84, 89, 84, 84, 84, 84, 81, 81, 50, 81, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 90, 90, 90, 90, 90, 90, 84, 84, 84, 84, 84, 84, 84, 81, 50, 50, 1, 84, 84, 84, 84] 90 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] 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, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 0 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451143 none CC1=CC(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)=NO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 24, 52, 90, 90, 90, 90, 90, 4, 4, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 90, 4, 4, 4, 4] 90 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451143 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451143 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451143/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451143 Building REAL300024451144 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451144' /scratch/stefan/7786230/working/building/REAL300024451144 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451144 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451144/0 /scratch/stefan/7786230/working/building/REAL300024451144 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1059 `/scratch/stefan/7786230/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451144/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451144 none CSCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 144, 117, 74, 117, 74, 74, 74, 74, 52, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 201, 201, 201, 144, 144, 144, 144, 74, 74, 74, 74, 74, 74, 74, 52, 29, 29, 1, 74, 74, 74, 74] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] 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, 42, 43, 44, 45]) total number of confs: 690 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451144 none CSCCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 14, 74, 74, 74, 74, 74, 1, 1, 26, 26, 26, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 74, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 22, 23, 36, 42, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451144 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451144 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451144/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451144 Building REAL300024451145 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451145' /scratch/stefan/7786230/working/building/REAL300024451145 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451145 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451145/0 /scratch/stefan/7786230/working/building/REAL300024451145 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1060 `/scratch/stefan/7786230/working/3D/1060' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C) `REAL300024451145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451145/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451145 none CC(C)CCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 181, 110, 78, 110, 78, 78, 78, 78, 52, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 78, 78, 78, 78, 78, 78, 78, 52, 30, 30, 1, 78, 78, 78, 78] 201 rigid atoms, others: [46, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 855 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451145 none CC(C)CCC(=O)N1CCCC(NC(=O)CSC2=NNC(=O)[N-]2)C1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 15, 18, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 20, 78, 78, 78, 78, 78, 1, 1, 18, 18, 17, 18, 18, 18, 18, 15, 15, 13, 13, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 78, 1, 2, 2, 2] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 12, 47, 40, 41, 23, 24, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 211 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451145 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451145 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451145/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451145 Building REAL300024451146 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451146' /scratch/stefan/7786230/working/building/REAL300024451146 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451146 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451146/0 /scratch/stefan/7786230/working/building/REAL300024451146 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1061 `/scratch/stefan/7786230/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=C1) `REAL300024451146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451146/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451146 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 105, 90, 90, 50, 90, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 120, 120, 201, 201, 201, 201, 105, 105, 105, 105, 105, 90, 50, 50, 1, 105, 105, 105, 105, 105, 105, 201, 201, 201] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 573 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: REAL300024451146 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 25, 25, 25, 78, 124, 201, 201, 201, 201, 201, 13, 13, 13, 11, 1, 11, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 25, 78, 78, 201, 13, 13, 13, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 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: 494 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451146 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)C1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 16, 39, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 2, 2, 2, 1, 1, 4, 16, 16, 105, 1, 1, 1, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451146 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451146 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451146/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451146 Building REAL300024451147 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451147' /scratch/stefan/7786230/working/building/REAL300024451147 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451147 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451147/0 /scratch/stefan/7786230/working/building/REAL300024451147 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1062 `/scratch/stefan/7786230/working/3D/1062' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1) `REAL300024451147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451147/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451147 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 49, 138, 138, 138, 138, 138, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 138, 1, 2, 2, 2, 9, 9] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 40, 35, 21, 22, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 245 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: REAL300024451147 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 169, 138, 169, 138, 138, 138, 138, 127, 127, 63, 127, 13, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 138, 127, 63, 63, 1, 138, 138, 138, 138, 201, 201] 201 rigid atoms, others: [39, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 629 number of broken/clashed sets: 1 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451147 none CC1=C(C(=O)N2CCCC(NC(=O)CSC3=NNC(=O)[N-]3)C2C)C=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 9, 9, 9, 9, 9, 13, 13, 13, 58, 112, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 13, 58, 58, 201, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 450 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451147 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451147 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451147/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451147 Building REAL300024451148 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451148' /scratch/stefan/7786230/working/building/REAL300024451148 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451148 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451148/0 /scratch/stefan/7786230/working/building/REAL300024451148 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1063 `/scratch/stefan/7786230/working/3D/1063' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1C=CCC1) `REAL300024451148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451148/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451148 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [72, 72, 51, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 101, 101, 153, 201, 201, 201, 201, 72, 72, 72, 72, 72, 51, 28, 28, 1, 72, 72, 72, 72, 72, 72, 153, 153, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 814 number of broken/clashed sets: 7 ./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: REAL300024451148 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 36, 36, 36, 104, 113, 201, 201, 201, 201, 201, 22, 22, 22, 19, 5, 19, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 36, 104, 104, 201, 22, 22, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 562 number of broken/clashed sets: 7 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451148 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CC1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 14, 17, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 3, 3, 12, 22, 22, 22, 22, 2, 2, 2, 1, 1, 5, 14, 14, 72, 1, 1, 1, 1, 1, 1, 12, 12, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451148 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451148 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451148/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451148 Building REAL300024451149 mkdir: created directory `/scratch/stefan/7786230/working/building/REAL300024451149' /scratch/stefan/7786230/working/building/REAL300024451149 /scratch/stefan/7786230/working /scratch/stefan/7786230 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300024451149 mkdir: created directory `0' /scratch/stefan/7786230/working/building/REAL300024451149/0 /scratch/stefan/7786230/working/building/REAL300024451149 /scratch/stefan/7786230/working /scratch/stefan/7786230 Protomer 0 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7786230/working/3D/1064 `/scratch/stefan/7786230/working/3D/1064' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=N1) `REAL300024451149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300024451149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7786230/working/building/REAL300024451149/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451149 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', '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, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 60, 45, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 88, 88, 172, 201, 201, 201, 201, 60, 60, 60, 60, 60, 45, 30, 30, 1, 60, 60, 60, 60, 60, 60, 172, 172, 201] 201 rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 752 number of broken/clashed sets: 14 ./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: REAL300024451149 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', '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, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 34, 34, 34, 107, 117, 201, 201, 201, 201, 201, 20, 20, 20, 19, 6, 19, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 34, 107, 107, 201, 20, 20, 20, 20, 20, 20, 6, 6, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 581 number of broken/clashed sets: 14 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300024451149 none CC1C(NC(=O)CSC2=NNC(=O)[N-]2)CCCN1C(=O)CN1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', '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, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 14, 16, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 3, 3, 13, 20, 20, 20, 20, 2, 2, 2, 1, 1, 4, 14, 14, 60, 1, 1, 1, 1, 1, 1, 13, 13, 20] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7786230/working/building/REAL300024451149 /scratch/stefan/7786230/working /scratch/stefan/7786230 Finished preparing REAL300024451149 Recording results /scratch/stefan/7786230/working /scratch/stefan/7786230 Appending to /scratch/stefan/7786230/finished/xaaaaef.* 0: /scratch/stefan/7786230/working/building/REAL300024451149/0.* Removing working files in /scratch/stefan/7786230/working/building/REAL300024451149 /scratch/stefan/7786230 Compressing combined databse files /scratch/stefan/7786230/finished/xaaaaef.db2.gz /scratch/stefan/7786230/finished/xaaaaef.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7786230/finished) ======================================================= Finalizing... removed `/scratch/stefan/7786230/working/3D/1065' removed directory: `/scratch/stefan/7786230/working/3D' `/scratch/stefan/7786230/working/protonate' -> `/scratch/stefan/7786230/archive' `/scratch/stefan/7786230/working/input-smiles.ism' -> `/scratch/stefan/7786230/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7786230/working/building' rmdir: removing directory, `/scratch/stefan/7786230/working' ls: No match. ls: No match.